[Swift-commit] r6099 - in SwiftTutorials/UofC_2012-11-27-fusion: . bin data scripts
davidk at ci.uchicago.edu
davidk at ci.uchicago.edu
Wed Dec 5 14:21:36 CST 2012
Author: davidk
Date: 2012-12-05 14:21:35 -0600 (Wed, 05 Dec 2012)
New Revision: 6099
Added:
SwiftTutorials/UofC_2012-11-27-fusion/README
SwiftTutorials/UofC_2012-11-27-fusion/bin/
SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup
SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh
SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist
SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh
SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp
SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl
SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh
SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift
SwiftTutorials/UofC_2012-11-27-fusion/bin/setup.sh
SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh
SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi
SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.c
SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh
SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf
SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb
SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf
SwiftTutorials/UofC_2012-11-27-fusion/data/
SwiftTutorials/UofC_2012-11-27-fusion/data/data.txt
SwiftTutorials/UofC_2012-11-27-fusion/par_cg_clath.inp
SwiftTutorials/UofC_2012-11-27-fusion/rmsd.temp.tcl
SwiftTutorials/UofC_2012-11-27-fusion/scripts/
SwiftTutorials/UofC_2012-11-27-fusion/scripts/catsn.swift
SwiftTutorials/UofC_2012-11-27-fusion/scripts/script01.swift
SwiftTutorials/UofC_2012-11-27-fusion/scripts/script02.swift
SwiftTutorials/UofC_2012-11-27-fusion/scripts/script03.swift
SwiftTutorials/UofC_2012-11-27-fusion/scripts/script04.swift
SwiftTutorials/UofC_2012-11-27-fusion/scripts/script05.swift
SwiftTutorials/UofC_2012-11-27-fusion/scripts/script06.swift
SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.kml
SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swift
SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swiftx
Log:
Files needed to run tutorials on fusion, with the additional of two new mpi examples
Added: SwiftTutorials/UofC_2012-11-27-fusion/README
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/README (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/README 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,100 @@
+
+INTRODUCTION TO SWIFT
+
+SETUP
+
+Obtain the tutorial package
+
+Change directory into the created directory called "tutorial"
+
+This directory contains:
+
+bin: script tools for the tutorial
+scripts: Swift scripts for the tutorial
+
+An output directory will be created by the Swift scripts
+
+
+Use bin/setup.sh to add tutorial programs to your PATH
+
+Run:
+
+source bin/setup.sh
+
+EXERCISE 1 - Run a simple command under Swift
+
+This script simply runs the getinfo command found in bin/getinfo.sh
+
+You can run this on the login node by typing:
+
+bin/getinfo.sh
+
+Inspect getinfo.sh to see what it does.
+
+The Swift syntax in scripts/script01.swift directs the output of
+getinfo.sh to file output/info.txt
+
+Run the Swift script by typing:
+
+runswift scripts/script01.swift
+
+Check that the output is created in the output directory
+
+EXERCISE 2 - Run parallel jobs
+
+The Swift syntax in scripts/script02.swift runs the getinfo
+script 25 times in parallel. Each job produces an output
+file with a different name.
+
+runswift scripts/script02.swift
+
+Check that the output is created successfully
+
+EXERCISE 3 - Run parallel jobs with pipelines
+
+The Swift syntax in scripts/script02.swift runs the getinfo
+script 25 times in parallel. Each job produces an output
+file with a different name. Each output file is then read by the
+filterinfo task, which produces output in _concurrent
+
+Inspect bin/filterinfo.sh to see what it does to the output of getinfo.sh
+
+runswift scripts/script03.swift
+
+EXERCISE 4 - Name files in pipelines
+
+In Exercise 3, the final outputs were named by Swift.
+Exercise 4 is similar to 3 but allows you to name the final
+outputs. Edit script04.swift to name the files in an appropriate
+way.
+
+EXERCISE 5 - Reduction
+
+Exercise 5 allows you to collect all of the filtered outputs
+and summarize them into one file. This Swift script allows
+suminfo.sh to read all the files and collect a statistic.
+
+Inspect bin/suminfo.sh to see what it will do to the files it reads.
+
+EXERCISE 6 - Simple MPI test
+
+Exercise 6 is a simple MPI test. Each rank of the MPI job
+runs a "hostname" command and creates a file. The files
+get added to a tar file - output/results.tar. A wrapper
+script, bin/testmpi.sh runs mpiexec to launch the test
+mpi program. This application uses the Fusion batch
+queue to request 2 nodes.
+
+View output/results.tar to see the results.
+
+EXERCISE 7 - NAMD MPI test
+
+Exercise 7 is a real application that runs NAMD
+using MPI. It is a simple parameter sweep that
+changes some values in the input files then does
+the run. Like exercise 6, this uses the batch queue
+with 2 nodes.
+
+CLEAN UP
+
+Simply run: bin/cleanup and enter y to confirm
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,17 @@
+#! /bin/sh
+
+echo Removing:
+echo
+ls -ltd script??-* swiftwork _concurrent output *.kml *.swiftx swift.log applist config sites.xml pathlist 2>/dev/null
+echo
+echo Enter y to proceed:
+read ok
+if [ _$ok = _y -o _$ok = _Y -o _$ok = _yes ]; then
+ echo
+ set -x
+ rm -rf script??-* swiftwork _concurrent output *.kml *.swiftx swift.log applist config sites.xml pathlist
+else
+ echo
+ echo No files removed.
+fi
+
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/cleanup
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,2 @@
+#! /bin/sh
+grep getinfo.sh $1 | wc -l >$2
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/filterinfo.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,10 @@
+cat <<END
+cluster cat /bin/cat null null null
+cluster sh /bin/sh null null null
+cluster getinfo $PWD/bin/getinfo.sh null null null
+cluster filterinfo $PWD/bin/filterinfo.sh null null null
+cluster suminfo $PWD/bin/suminfo.sh null null null
+clustermpi rmsd $PWD/bin/rmsd.sh null null null
+clustermpi plot_pd $PWD/bin/plot_pd.pl null null null
+clustermpi testmpi $PWD/bin/testmpi.sh null null null
+END
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/genapplist
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,6 @@
+#! /bin/sh
+
+hostname -f
+date
+sleep 2
+ps -u $USER -H
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/getinfo.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,6 @@
+#! /bin/sh
+
+hostname -f
+date
+sleep 3
+ps -u $USER -H -f
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/myapp
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,70 @@
+#!/usr/bin/env perl
+
+use strict;
+use warnings;
+
+# This code will run many short simulations in order to
+# sweep the nonbonded parameter space
+
+# File names
+open (OFILE, ">", "output/rmsd_pd.dat");
+
+# Bead names
+my $b1name = "PX";
+my $b2name = "DT";
+
+# Bead ranges
+my $b1min=0.0;
+my $b1max=10.0;
+
+my $b2min=0.0;
+my $b2max=10.0;
+
+my $del=0.50;
+
+# Set large number to find RMSD min
+my $rmsdmin = 123456789.0;
+my $b1rmsdmin=0.0;
+my $b2rmsdmin=0.0;
+
+my $b1=$b1min;
+
+while ($b1<=$b1max)
+{
+ my $b2=$b2min;
+
+ while ($b2<=$b2max)
+ {
+ if (-s "output/rmsd.$b1name${b1}_$b2name${b2}.dat")
+ {
+ open(INPUT, "<", "output/rmsd.$b1name${b1}_$b2name${b2}.dat");
+ $_ = <INPUT>;
+
+ my @data = split(/ +/,$_);
+ my $rmsd=$data[2]*1.0;
+
+ # Find Minimum
+ if ($rmsd<$rmsdmin)
+ {
+ $rmsdmin=$rmsd;
+ $b1rmsdmin=$b1;
+ $b2rmsdmin=$b2;
+ }
+
+ print OFILE "$b1 $b2 $rmsd\n";
+ close(INPUT);
+ }
+
+ $b2 = $b2+$del;
+
+ }
+
+ print OFILE " \n";
+ $b1 = $b1+$del;
+
+}
+
+close(OFILE);
+
+print "Minimum Values\n";
+print "RMSD = $rmsdmin, eps_$b1name = $b1rmsdmin, eps_$b2name = $b2rmsdmin\n" ;
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/plot_pd.pl
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,47 @@
+#!/bin/bash
+
+b1=$1
+b2=$2
+b1name=$3
+b2name=$4
+namd_input=$5
+namd_parameters=$6
+vmd_script=$7
+
+echo Command line arguments: $@
+echo
+
+echo Hostname: $( hostname )
+echo
+
+echo File listing
+echo ------------
+find
+echo
+
+echo Running the following sed commands
+echo sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ -e s at __DIR__@$PWD@ $namd_input
+echo sed -i -e s/BLAB1/$b1name$b1/ -e s/BLAB2/$b2name$b2/ -e s at __DIR__@$PWD@ $namd_input
+echo sed -i -e s/HBEPS/-0.01/g -e s/PXEPS/-$b1/g -e s/DTEPS/-$b2/g -e s/AKEPS/-0.01/g -e s/LTEPS/-0.01/g $namd_parameters
+sed -i -e s/BLAB1/$b1name$b1/g -e s/BLAB2/$b2name$b2/g -e s/B1/$b1/ -e s/B2/$b2/ $vmd_script
+sed -i -e s/HBEPS/-0.01/g -e s/PXEPS/-$b1/g -e s/DTEPS/-$b2/g -e s/AKEPS/-0.01/g -e s/LTEPS/-0.01/g $namd_parameters
+sed -i -e s/BLAB1/$b1name$b1/g -e s/BLAB2/$b2name$b2/g -e s/B1/$b1/ -e s/B2/$b2/ $vmd_script
+echo Done with sed
+echo
+
+namd2=$( which namd2 )
+echo Found namd2 at $namd2
+echo About to run mpiexec -machinefile $PBS_NODEFILE $namd2 $namd_input
+mpiexec -machinefile $PBS_NODEFILE $namd2 $namd_input
+
+echo
+echo About to run vmd -dispdev text -e $vmd_script
+vmd -dispdev text -e $vmd_script
+
+mv output/cg_clath_cage.dcd output/cg_clath_cage-$b1-$b2.dcd
+mv rmsd.dat output/rmsd.$b1name${b1}_$b2name${b2}.dat
+
+echo
+echo Files at end of run
+find
+echo
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/rmsd.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,75 @@
+#! /bin/sh
+
+cat <<END >pathlist
+rule .*_concurrent/.* DIRECT $PWD/tmp
+rule .* DIRECT /
+END
+
+cat <<END >config
+status.mode=provider
+use.provider.staging=false
+use.wrapper.staging=false
+wrapperlog.always.transfer=true
+execution.retries=0
+lazy.errors=false
+provider.staging.pin.swiftfiles=false
+sitedir.keep=true
+file.gc.enabled=false
+tcp.port.range=50000,51000
+END
+
+reservationID=${reservationID:-swift}
+
+cat <<END >sites.xml
+
+<config>
+
+<pool handle="local">
+ <execution provider="local"/>
+ <profile namespace="karajan" key="jobThrottle">0.03</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <filesystem provider="local" url="none" />
+ <workdirectory>$PWD/swiftwork</workdirectory>
+</pool>
+
+<pool handle="cluster">
+ <execution jobmanager="local:pbs" provider="coaster" url="none"/>
+ <filesystem provider="local" url="none" />
+ <profile namespace="globus" key="maxtime">3600</profile>
+ <profile namespace="globus" key="jobsPerNode">8</profile>
+ <profile namespace="globus" key="queue">shared</profile>
+ <profile namespace="globus" key="nodeGranularity">1</profile>
+ <profile namespace="globus" key="maxNodes">1</profile>
+ <profile namespace="karajan" key="jobThrottle">1.0</profile>
+ <profile namespace="karajan" key="initialScore">100</profile>
+ <profile namespace="globus" key="HighOverAllocation">100</profile>
+ <profile namespace="globus" key="LowOverAllocation">100</profile>
+ <workdirectory>$PWD/swiftwork</workdirectory>
+</pool>
+
+<pool handle="clustermpi">
+ <execution jobmanager="local:pbs" provider="pbs" url="none"/>
+ <filesystem provider="local" url="none" />
+ <profile namespace="globus" key="maxtime">60</profile>
+ <profile namespace="globus" key="jobsPerNode">1</profile>
+ <profile namespace="globus" key="ppn">8</profile>
+ <profile namespace="karajan" key="jobThrottle">5.99</profile>
+ <profile namespace="karajan" key="initialScore">10000</profile>
+ <profile namespace="globus" key="count">2</profile>
+ <profile namespace="globus" key="jobType">single</profile>
+ <workdirectory>$PWD/swiftwork</workdirectory>
+</pool>
+
+</config>
+
+END
+
+genapplist >applist
+
+set -x
+#swift -config config -tc.file applist -sites.file sites.xml -cdm.file pathlist $*
+swift -config config -tc.file applist -sites.file sites.xml $*
+
+
+
+
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/runswift
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/setup.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/setup.sh (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/setup.sh 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1 @@
+PATH=/homes/davidk/swift-0.94/cog/modules/swift/dist/swift-svn/bin:/homes/davidk/namd_2.8-intel-openmpi:/homes/davidk/vmd:$PWD/bin:$PATH
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,2 @@
+#! /bin/sh
+awk '{ sum += $1 } END { print "Total processes observed: " sum }' $*
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/suminfo.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi
===================================================================
(Binary files differ)
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.c
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.c (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.c 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,51 @@
+#include <stdio.h>
+#include <stdlib.h>
+#include <mpi.h>
+#include <string.h>
+
+int main (argc, argv)
+ int argc;
+ char *argv[];
+{
+ int rank, size;
+
+ MPI_Init (&argc, &argv); /* starts MPI */
+ MPI_Comm_rank (MPI_COMM_WORLD, &rank); /* get current process id */
+ MPI_Comm_size (MPI_COMM_WORLD, &size); /* get number of processes */
+
+ FILE *fp, *command;
+ char filename[100];
+ char hostname[1024];
+
+ sprintf(filename, "output.%d.txt", rank);
+ printf("Trying to write output to %s\n", filename);
+ fp = fopen(filename, "w");
+
+ if (fp == NULL) {
+ printf("Unable to write file\n");
+ exit(0);
+ }
+
+ command = popen("/bin/hostname -f", "r");
+ if(command == NULL) {
+ printf("Failed to run command\n");
+ exit(1);
+ }
+
+ while (fgets(hostname, sizeof(hostname)-1, command) != NULL) {
+ hostname[(strlen(hostname)-1)] = '\0';
+ fprintf(fp, "Hostname: %s, rank: %d\n", hostname, rank);
+ }
+
+ fclose(fp);
+ printf("Done writing output file %s\n", filename);
+
+ MPI_Finalize();
+
+ // Create a tar file of results (only once)
+ if(rank == 0) {
+ system("mkdir output");
+ system("tar cvf output/results.tar output*.txt");
+ }
+ return 0;
+}
Added: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,3 @@
+#!/bin/bash
+
+mpiexec -machinefile $PBS_NODEFILE /homes/davidk/testmpi/testmpi
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/bin/testmpi.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,83 @@
+# NAMD Config file - autogenerated by NAMDgui plugin
+# Author: Jan Saam, saam at charite.de
+
+# input
+coordinates cg_clath_cage.pdb
+structure cg_clath_cage.psf
+parameters par_cg_clath.inp
+paratypecharmm on
+
+# output
+set output output/cg_clath_cage
+outputname $output
+dcdfile ${output}.dcd
+xstFile ${output}.xst
+dcdfreq 1000
+xstFreq 1000
+
+binaryoutput yes
+binaryrestart yes
+outputEnergies 1000
+restartfreq 1000
+
+fixedAtoms off
+
+# Basic dynamics
+exclude scaled1-4
+1-4scaling 1
+COMmotion no
+dielectric 1.0
+
+
+# Simulation space partitioning
+cutoff 350
+switching on
+switchdist 348
+pairlistdist 352
+
+# Multiple timestepping
+firsttimestep 0
+timestep 10
+stepspercycle 1
+nonbondedFreq 1
+fullElectFrequency 1
+rigidBonds all
+
+# Temperature control
+
+set temperature 310
+temperature $temperature; # initial temperature
+
+# Langevin Dynamics
+langevin on; # do langevin dynamics
+langevinDamping 0.001 # damping coefficient (gamma) of 1/ps
+langevinTemp $temperature; # bath temperature
+langevinHydrogen no; # don't couple langevin bath to hydrogens
+
+
+
+# Scripting
+
+# Simulated Annealing
+#reassignFreq 10000
+#reassignTemp 310
+#minimize 10000
+#for { set TEMP 310 } { $TEMP <= 650 } { incr TEMP 5 } {
+# run 10000
+# reassignTemp $TEMP
+# langevinTemp $TEMP
+#}
+#
+#run 1000000
+#
+#for { set TEMP 650 } { $TEMP >= 310 } { incr TEMP -5 } {
+# reassignTemp $TEMP
+# langevinTemp $TEMP
+# run 10000
+#}
+#run 1000000
+
+minimize 1000
+reinitvels $temperature
+run 2000
+
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.conf
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,470 @@
+REMARK original generated coordinate pdb file
+ATOM 1 HB0 CLA X 1 92.981 164.025 331.473 1.00 0.00 A0
+ATOM 2 PX1 CLA X 1 136.274 211.422 275.579 1.00 0.00 A0
+ATOM 3 DT1 CLA X 1 200.662 208.148 159.192 1.00 0.00 A0
+ATOM 4 AK1 CLA X 1 243.304 111.359 96.656 1.00 0.00 A0
+ATOM 5 LT1 CLA X 1 223.763 18.662 85.497 1.00 0.00 A0
+ATOM 6 PX2 CLA X 1 126.815 89.000 352.917 1.00 0.00 A0
+ATOM 7 DT2 CLA X 1 128.673 -47.724 333.137 1.00 0.00 A0
+ATOM 8 AK2 CLA X 1 49.929-132.718 287.973 1.00 0.00 A0
+ATOM 9 LT2 CLA X 1 -24.828-143.462 235.435 1.00 0.00 A0
+ATOM 10 PX3 CLA X 1 10.483 180.619 340.613 1.00 0.00 A0
+ATOM 11 DT3 CLA X 1 -95.424 204.239 265.860 1.00 0.00 A0
+ATOM 12 AK3 CLA X 1 -101.877 231.712 146.926 1.00 0.00 A0
+ATOM 13 LT3 CLA X 1 -58.664 217.336 66.678 1.00 0.00 A0
+ATOM 14 HB0 CLA X 1 152.597 263.250 182.367 1.00 0.00 B0
+ATOM 15 PX1 CLA X 1 120.437 238.824 256.749 1.00 0.00 B0
+ATOM 16 DT1 CLA X 1 18.642 174.399 313.695 1.00 0.00 B0
+ATOM 17 AK1 CLA X 1 -88.420 151.452 262.690 1.00 0.00 B0
+ATOM 18 LT1 CLA X 1 -128.527 143.156 177.443 1.00 0.00 B0
+ATOM 19 PX2 CLA X 1 99.230 306.155 133.576 1.00 0.00 B0
+ATOM 20 DT2 CLA X 1 21.433 316.316 21.125 1.00 0.00 B0
+ATOM 21 AK2 CLA X 1 26.263 266.923 -95.151 1.00 0.00 B0
+ATOM 22 LT2 CLA X 1 58.151 195.850-145.576 1.00 0.00 B0
+ATOM 23 PX3 CLA X 1 223.451 225.604 155.002 1.00 0.00 B0
+ATOM 24 DT3 CLA X 1 275.701 105.136 138.751 1.00 0.00 B0
+ATOM 25 AK3 CLA X 1 235.267 1.374 186.863 1.00 0.00 B0
+ATOM 26 LT3 CLA X 1 155.819 -36.632 217.712 1.00 0.00 B0
+ATOM 27 HB0 CLA X 1 286.805 165.855 93.118 1.00 0.00 C0
+ATOM 28 PX1 CLA X 1 303.935 101.204 144.420 1.00 0.00 C0
+ATOM 29 DT1 CLA X 1 251.178 21.712 232.998 1.00 0.00 C0
+ATOM 30 AK1 CLA X 1 142.263 28.038 287.691 1.00 0.00 C0
+ATOM 31 LT1 CLA X 1 50.945 58.195 270.101 1.00 0.00 C0
+ATOM 32 PX2 CLA X 1 234.620 227.534 121.486 1.00 0.00 C0
+ATOM 33 DT2 CLA X 1 104.398 278.700 124.820 1.00 0.00 C0
+ATOM 34 AK2 CLA X 1 0.965 276.330 50.135 1.00 0.00 C0
+ATOM 35 LT2 CLA X 1 -42.600 228.187 -18.776 1.00 0.00 C0
+ATOM 36 PX3 CLA X 1 303.934 158.846 11.493 1.00 0.00 C0
+ATOM 37 DT3 CLA X 1 291.514 88.537-103.359 1.00 0.00 C0
+ATOM 38 AK3 CLA X 1 250.991 -24.248-144.395 1.00 0.00 C0
+ATOM 39 LT3 CLA X 1 191.706 -94.728-126.760 1.00 0.00 C0
+ATOM 40 HB0 CLA X 1 -95.559 162.537 331.473 1.00 0.00 A1
+ATOM 41 PX1 CLA X 1 -114.959 223.728 275.579 1.00 0.00 A1
+ATOM 42 DT1 CLA X 1 -79.930 277.853 159.192 1.00 0.00 A1
+ATOM 43 AK1 CLA X 1 25.213 266.386 96.656 1.00 0.00 A1
+ATOM 44 LT1 CLA X 1 95.719 203.115 85.497 1.00 0.00 A1
+ATOM 45 PX2 CLA X 1 -13.669 154.325 352.917 1.00 0.00 A1
+ATOM 46 DT2 CLA X 1 105.666 87.572 333.137 1.00 0.00 A1
+ATOM 47 AK2 CLA X 1 139.902 -23.120 287.973 1.00 0.00 A1
+ATOM 48 LT2 CLA X 1 111.827 -93.233 235.435 1.00 0.00 A1
+ATOM 49 PX3 CLA X 1 -151.180 99.388 340.613 1.00 0.00 A1
+ATOM 50 DT3 CLA X 1 -224.588 19.480 265.860 1.00 0.00 A1
+ATOM 51 AK3 CLA X 1 -251.607 27.627 146.926 1.00 0.00 A1
+ATOM 52 LT3 CLA X 1 -217.550 57.864 66.678 1.00 0.00 A1
+ATOM 53 HB0 CLA X 1 -151.683 263.777 182.367 1.00 0.00 B1
+ATOM 54 PX1 CLA X 1 -146.609 223.714 256.749 1.00 0.00 B1
+ATOM 55 DT1 CLA X 1 -141.713 103.344 313.695 1.00 0.00 B1
+ATOM 56 AK1 CLA X 1 -175.371 -0.848 262.690 1.00 0.00 B1
+ATOM 57 LT1 CLA X 1 -188.241 -39.730 177.443 1.00 0.00 B1
+ATOM 58 PX2 CLA X 1 -215.523 239.014 133.576 1.00 0.00 B1
+ATOM 59 DT2 CLA X 1 -263.221 176.720 21.125 1.00 0.00 B1
+ATOM 60 AK2 CLA X 1 -218.030 156.206 -95.151 1.00 0.00 B1
+ATOM 61 LT2 CLA X 1 -140.536 148.285-145.576 1.00 0.00 B1
+ATOM 62 PX3 CLA X 1 -83.654 306.316 155.002 1.00 0.00 B1
+ATOM 63 DT3 CLA X 1 46.800 291.332 138.751 1.00 0.00 B1
+ATOM 64 AK3 CLA X 1 116.444 204.434 186.863 1.00 0.00 B1
+ATOM 65 LT3 CLA X 1 109.634 116.627 217.712 1.00 0.00 B1
+ATOM 66 HB0 CLA X 1 -0.232 331.308 93.118 1.00 0.00 C1
+ATOM 67 PX1 CLA X 1 64.322 313.817 144.420 1.00 0.00 C1
+ATOM 68 DT1 CLA X 1 106.786 228.382 232.998 1.00 0.00 C1
+ATOM 69 AK1 CLA X 1 46.850 137.222 287.691 1.00 0.00 C1
+ATOM 70 LT1 CLA X 1 -24.926 73.217 270.101 1.00 0.00 C1
+ATOM 71 PX2 CLA X 1 -79.740 316.953 121.486 1.00 0.00 C1
+ATOM 72 DT2 CLA X 1 -189.163 229.761 124.820 1.00 0.00 C1
+ATOM 73 AK2 CLA X 1 -238.827 139.001 50.135 1.00 0.00 C1
+ATOM 74 LT2 CLA X 1 -218.915 77.201 -18.776 1.00 0.00 C1
+ATOM 75 PX3 CLA X 1 14.402 342.637 11.493 1.00 0.00 C1
+ATOM 76 DT3 CLA X 1 69.082 296.727-103.359 1.00 0.00 C1
+ATOM 77 AK3 CLA X 1 146.495 205.240-144.395 1.00 0.00 C1
+ATOM 78 LT3 CLA X 1 177.890 118.659-126.760 1.00 0.00 C1
+ATOM 79 HB0 CLA X 1 -188.541 -1.488 331.473 1.00 0.00 A2
+ATOM 80 PX1 CLA X 1 -251.234 12.306 275.579 1.00 0.00 A2
+ATOM 81 DT1 CLA X 1 -280.592 69.705 159.192 1.00 0.00 A2
+ATOM 82 AK1 CLA X 1 -218.091 155.028 96.656 1.00 0.00 A2
+ATOM 83 LT1 CLA X 1 -128.043 184.453 85.497 1.00 0.00 A2
+ATOM 84 PX2 CLA X 1 -140.484 65.324 352.917 1.00 0.00 A2
+ATOM 85 DT2 CLA X 1 -23.007 135.296 333.137 1.00 0.00 A2
+ATOM 86 AK2 CLA X 1 89.973 109.599 287.973 1.00 0.00 A2
+ATOM 87 LT2 CLA X 1 136.656 50.229 235.435 1.00 0.00 A2
+ATOM 88 PX3 CLA X 1 -161.662 -81.231 340.613 1.00 0.00 A2
+ATOM 89 DT3 CLA X 1 -129.164-184.759 265.860 1.00 0.00 A2
+ATOM 90 AK3 CLA X 1 -149.729-204.084 146.926 1.00 0.00 A2
+ATOM 91 LT3 CLA X 1 -158.887-159.472 66.678 1.00 0.00 A2
+ATOM 92 HB0 CLA X 1 -304.279 0.528 182.367 1.00 0.00 B2
+ATOM 93 PX1 CLA X 1 -267.047 -15.111 256.749 1.00 0.00 B2
+ATOM 94 DT1 CLA X 1 -160.355 -71.055 313.695 1.00 0.00 B2
+ATOM 95 AK1 CLA X 1 -86.951-152.300 262.690 1.00 0.00 B2
+ATOM 96 LT1 CLA X 1 -59.713-182.886 177.443 1.00 0.00 B2
+ATOM 97 PX2 CLA X 1 -314.754 -67.142 133.576 1.00 0.00 B2
+ATOM 98 DT2 CLA X 1 -284.654-139.597 21.125 1.00 0.00 B2
+ATOM 99 AK2 CLA X 1 -244.294-110.717 -95.151 1.00 0.00 B2
+ATOM 100 LT2 CLA X 1 -198.687 -47.565-145.576 1.00 0.00 B2
+ATOM 101 PX3 CLA X 1 -307.104 80.712 155.002 1.00 0.00 B2
+ATOM 102 DT3 CLA X 1 -228.901 186.196 138.751 1.00 0.00 B2
+ATOM 103 AK3 CLA X 1 -118.823 203.060 186.863 1.00 0.00 B2
+ATOM 104 LT3 CLA X 1 -46.185 153.259 217.712 1.00 0.00 B2
+ATOM 105 HB0 CLA X 1 -287.037 165.452 93.118 1.00 0.00 C2
+ATOM 106 PX1 CLA X 1 -239.613 212.613 144.420 1.00 0.00 C2
+ATOM 107 DT1 CLA X 1 -144.392 206.670 232.998 1.00 0.00 C2
+ATOM 108 AK1 CLA X 1 -95.413 109.184 287.691 1.00 0.00 C2
+ATOM 109 LT1 CLA X 1 -75.871 15.022 270.101 1.00 0.00 C2
+ATOM 110 PX2 CLA X 1 -314.360 89.420 121.486 1.00 0.00 C2
+ATOM 111 DT2 CLA X 1 -293.560 -48.939 124.820 1.00 0.00 C2
+ATOM 112 AK2 CLA X 1 -239.791-137.330 50.135 1.00 0.00 C2
+ATOM 113 LT2 CLA X 1 -176.315-150.986 -18.776 1.00 0.00 C2
+ATOM 114 PX3 CLA X 1 -289.532 183.791 11.493 1.00 0.00 C2
+ATOM 115 DT3 CLA X 1 -222.432 208.190-103.359 1.00 0.00 C2
+ATOM 116 AK3 CLA X 1 -104.496 229.489-144.395 1.00 0.00 C2
+ATOM 117 LT3 CLA X 1 -13.817 213.386-126.760 1.00 0.00 C2
+ATOM 118 HB0 CLA X 1 -92.981-164.025 331.473 1.00 0.00 A3
+ATOM 119 PX1 CLA X 1 -136.274-211.422 275.579 1.00 0.00 A3
+ATOM 120 DT1 CLA X 1 -200.662-208.148 159.192 1.00 0.00 A3
+ATOM 121 AK1 CLA X 1 -243.304-111.359 96.656 1.00 0.00 A3
+ATOM 122 LT1 CLA X 1 -223.763 -18.662 85.497 1.00 0.00 A3
+ATOM 123 PX2 CLA X 1 -126.815 -89.000 352.917 1.00 0.00 A3
+ATOM 124 DT2 CLA X 1 -128.673 47.724 333.137 1.00 0.00 A3
+ATOM 125 AK2 CLA X 1 -49.929 132.718 287.973 1.00 0.00 A3
+ATOM 126 LT2 CLA X 1 24.828 143.462 235.435 1.00 0.00 A3
+ATOM 127 PX3 CLA X 1 -10.483-180.619 340.613 1.00 0.00 A3
+ATOM 128 DT3 CLA X 1 95.424-204.239 265.860 1.00 0.00 A3
+ATOM 129 AK3 CLA X 1 101.877-231.712 146.926 1.00 0.00 A3
+ATOM 130 LT3 CLA X 1 58.664-217.336 66.678 1.00 0.00 A3
+ATOM 131 HB0 CLA X 1 -152.597-263.250 182.367 1.00 0.00 B3
+ATOM 132 PX1 CLA X 1 -120.437-238.824 256.749 1.00 0.00 B3
+ATOM 133 DT1 CLA X 1 -18.642-174.399 313.695 1.00 0.00 B3
+ATOM 134 AK1 CLA X 1 88.420-151.452 262.690 1.00 0.00 B3
+ATOM 135 LT1 CLA X 1 128.527-143.156 177.443 1.00 0.00 B3
+ATOM 136 PX2 CLA X 1 -99.230-306.155 133.576 1.00 0.00 B3
+ATOM 137 DT2 CLA X 1 -21.433-316.316 21.125 1.00 0.00 B3
+ATOM 138 AK2 CLA X 1 -26.263-266.923 -95.151 1.00 0.00 B3
+ATOM 139 LT2 CLA X 1 -58.151-195.850-145.576 1.00 0.00 B3
+ATOM 140 PX3 CLA X 1 -223.451-225.604 155.002 1.00 0.00 B3
+ATOM 141 DT3 CLA X 1 -275.701-105.136 138.751 1.00 0.00 B3
+ATOM 142 AK3 CLA X 1 -235.267 -1.374 186.863 1.00 0.00 B3
+ATOM 143 LT3 CLA X 1 -155.819 36.632 217.712 1.00 0.00 B3
+ATOM 144 HB0 CLA X 1 -286.805-165.855 93.118 1.00 0.00 C3
+ATOM 145 PX1 CLA X 1 -303.935-101.204 144.420 1.00 0.00 C3
+ATOM 146 DT1 CLA X 1 -251.178 -21.712 232.998 1.00 0.00 C3
+ATOM 147 AK1 CLA X 1 -142.263 -28.038 287.691 1.00 0.00 C3
+ATOM 148 LT1 CLA X 1 -50.945 -58.195 270.101 1.00 0.00 C3
+ATOM 149 PX2 CLA X 1 -234.620-227.534 121.486 1.00 0.00 C3
+ATOM 150 DT2 CLA X 1 -104.398-278.700 124.820 1.00 0.00 C3
+ATOM 151 AK2 CLA X 1 -0.965-276.330 50.135 1.00 0.00 C3
+ATOM 152 LT2 CLA X 1 42.600-228.187 -18.776 1.00 0.00 C3
+ATOM 153 PX3 CLA X 1 -303.934-158.846 11.493 1.00 0.00 C3
+ATOM 154 DT3 CLA X 1 -291.514 -88.537-103.359 1.00 0.00 C3
+ATOM 155 AK3 CLA X 1 -250.991 24.248-144.395 1.00 0.00 C3
+ATOM 156 LT3 CLA X 1 -191.706 94.728-126.760 1.00 0.00 C3
+ATOM 157 HB0 CLA X 1 95.559-162.537 331.473 1.00 0.00 A4
+ATOM 158 PX1 CLA X 1 114.959-223.728 275.579 1.00 0.00 A4
+ATOM 159 DT1 CLA X 1 79.930-277.853 159.192 1.00 0.00 A4
+ATOM 160 AK1 CLA X 1 -25.213-266.386 96.656 1.00 0.00 A4
+ATOM 161 LT1 CLA X 1 -95.719-203.115 85.497 1.00 0.00 A4
+ATOM 162 PX2 CLA X 1 13.669-154.325 352.917 1.00 0.00 A4
+ATOM 163 DT2 CLA X 1 -105.666 -87.572 333.137 1.00 0.00 A4
+ATOM 164 AK2 CLA X 1 -139.902 23.120 287.973 1.00 0.00 A4
+ATOM 165 LT2 CLA X 1 -111.827 93.233 235.435 1.00 0.00 A4
+ATOM 166 PX3 CLA X 1 151.180 -99.388 340.613 1.00 0.00 A4
+ATOM 167 DT3 CLA X 1 224.588 -19.480 265.860 1.00 0.00 A4
+ATOM 168 AK3 CLA X 1 251.607 -27.627 146.926 1.00 0.00 A4
+ATOM 169 LT3 CLA X 1 217.550 -57.864 66.678 1.00 0.00 A4
+ATOM 170 HB0 CLA X 1 151.683-263.777 182.367 1.00 0.00 B4
+ATOM 171 PX1 CLA X 1 146.609-223.714 256.749 1.00 0.00 B4
+ATOM 172 DT1 CLA X 1 141.713-103.344 313.695 1.00 0.00 B4
+ATOM 173 AK1 CLA X 1 175.371 0.848 262.690 1.00 0.00 B4
+ATOM 174 LT1 CLA X 1 188.241 39.730 177.443 1.00 0.00 B4
+ATOM 175 PX2 CLA X 1 215.523-239.014 133.576 1.00 0.00 B4
+ATOM 176 DT2 CLA X 1 263.221-176.720 21.125 1.00 0.00 B4
+ATOM 177 AK2 CLA X 1 218.030-156.206 -95.151 1.00 0.00 B4
+ATOM 178 LT2 CLA X 1 140.536-148.285-145.576 1.00 0.00 B4
+ATOM 179 PX3 CLA X 1 83.654-306.316 155.002 1.00 0.00 B4
+ATOM 180 DT3 CLA X 1 -46.800-291.332 138.751 1.00 0.00 B4
+ATOM 181 AK3 CLA X 1 -116.444-204.434 186.863 1.00 0.00 B4
+ATOM 182 LT3 CLA X 1 -109.634-116.627 217.712 1.00 0.00 B4
+ATOM 183 HB0 CLA X 1 0.232-331.308 93.118 1.00 0.00 C4
+ATOM 184 PX1 CLA X 1 -64.322-313.817 144.420 1.00 0.00 C4
+ATOM 185 DT1 CLA X 1 -106.786-228.382 232.998 1.00 0.00 C4
+ATOM 186 AK1 CLA X 1 -46.850-137.222 287.691 1.00 0.00 C4
+ATOM 187 LT1 CLA X 1 24.926 -73.217 270.101 1.00 0.00 C4
+ATOM 188 PX2 CLA X 1 79.740-316.953 121.486 1.00 0.00 C4
+ATOM 189 DT2 CLA X 1 189.163-229.761 124.820 1.00 0.00 C4
+ATOM 190 AK2 CLA X 1 238.827-139.001 50.135 1.00 0.00 C4
+ATOM 191 LT2 CLA X 1 218.915 -77.201 -18.776 1.00 0.00 C4
+ATOM 192 PX3 CLA X 1 -14.402-342.637 11.493 1.00 0.00 C4
+ATOM 193 DT3 CLA X 1 -69.082-296.727-103.359 1.00 0.00 C4
+ATOM 194 AK3 CLA X 1 -146.495-205.240-144.395 1.00 0.00 C4
+ATOM 195 LT3 CLA X 1 -177.890-118.659-126.760 1.00 0.00 C4
+ATOM 196 HB0 CLA X 1 188.541 1.488 331.473 1.00 0.00 A5
+ATOM 197 PX1 CLA X 1 251.234 -12.306 275.579 1.00 0.00 A5
+ATOM 198 DT1 CLA X 1 280.592 -69.705 159.192 1.00 0.00 A5
+ATOM 199 AK1 CLA X 1 218.091-155.028 96.656 1.00 0.00 A5
+ATOM 200 LT1 CLA X 1 128.043-184.453 85.497 1.00 0.00 A5
+ATOM 201 PX2 CLA X 1 140.484 -65.324 352.917 1.00 0.00 A5
+ATOM 202 DT2 CLA X 1 23.007-135.296 333.137 1.00 0.00 A5
+ATOM 203 AK2 CLA X 1 -89.973-109.599 287.973 1.00 0.00 A5
+ATOM 204 LT2 CLA X 1 -136.656 -50.229 235.435 1.00 0.00 A5
+ATOM 205 PX3 CLA X 1 161.662 81.231 340.613 1.00 0.00 A5
+ATOM 206 DT3 CLA X 1 129.164 184.759 265.860 1.00 0.00 A5
+ATOM 207 AK3 CLA X 1 149.729 204.084 146.926 1.00 0.00 A5
+ATOM 208 LT3 CLA X 1 158.887 159.472 66.678 1.00 0.00 A5
+ATOM 209 HB0 CLA X 1 304.279 -0.528 182.367 1.00 0.00 B5
+ATOM 210 PX1 CLA X 1 267.047 15.111 256.749 1.00 0.00 B5
+ATOM 211 DT1 CLA X 1 160.355 71.055 313.695 1.00 0.00 B5
+ATOM 212 AK1 CLA X 1 86.951 152.300 262.690 1.00 0.00 B5
+ATOM 213 LT1 CLA X 1 59.713 182.886 177.443 1.00 0.00 B5
+ATOM 214 PX2 CLA X 1 314.754 67.142 133.576 1.00 0.00 B5
+ATOM 215 DT2 CLA X 1 284.654 139.597 21.125 1.00 0.00 B5
+ATOM 216 AK2 CLA X 1 244.294 110.717 -95.151 1.00 0.00 B5
+ATOM 217 LT2 CLA X 1 198.687 47.565-145.576 1.00 0.00 B5
+ATOM 218 PX3 CLA X 1 307.104 -80.712 155.002 1.00 0.00 B5
+ATOM 219 DT3 CLA X 1 228.901-186.196 138.751 1.00 0.00 B5
+ATOM 220 AK3 CLA X 1 118.823-203.060 186.863 1.00 0.00 B5
+ATOM 221 LT3 CLA X 1 46.185-153.259 217.712 1.00 0.00 B5
+ATOM 222 HB0 CLA X 1 287.037-165.452 93.118 1.00 0.00 C5
+ATOM 223 PX1 CLA X 1 239.613-212.613 144.420 1.00 0.00 C5
+ATOM 224 DT1 CLA X 1 144.392-206.670 232.998 1.00 0.00 C5
+ATOM 225 AK1 CLA X 1 95.413-109.184 287.691 1.00 0.00 C5
+ATOM 226 LT1 CLA X 1 75.871 -15.022 270.101 1.00 0.00 C5
+ATOM 227 PX2 CLA X 1 314.360 -89.420 121.486 1.00 0.00 C5
+ATOM 228 DT2 CLA X 1 293.560 48.939 124.820 1.00 0.00 C5
+ATOM 229 AK2 CLA X 1 239.791 137.330 50.135 1.00 0.00 C5
+ATOM 230 LT2 CLA X 1 176.315 150.986 -18.776 1.00 0.00 C5
+ATOM 231 PX3 CLA X 1 289.532-183.791 11.493 1.00 0.00 C5
+ATOM 232 DT3 CLA X 1 222.432-208.190-103.359 1.00 0.00 C5
+ATOM 233 AK3 CLA X 1 104.496-229.489-144.395 1.00 0.00 C5
+ATOM 234 LT3 CLA X 1 13.817-213.386-126.760 1.00 0.00 C5
+ATOM 235 HB0 CLA X 1 95.559 162.537-331.473 1.00 0.00 A6
+ATOM 236 PX1 CLA X 1 114.959 223.728-275.579 1.00 0.00 A6
+ATOM 237 DT1 CLA X 1 79.930 277.853-159.192 1.00 0.00 A6
+ATOM 238 AK1 CLA X 1 -25.213 266.386 -96.656 1.00 0.00 A6
+ATOM 239 LT1 CLA X 1 -95.719 203.115 -85.497 1.00 0.00 A6
+ATOM 240 PX2 CLA X 1 13.669 154.325-352.917 1.00 0.00 A6
+ATOM 241 DT2 CLA X 1 -105.666 87.572-333.137 1.00 0.00 A6
+ATOM 242 AK2 CLA X 1 -139.902 -23.120-287.973 1.00 0.00 A6
+ATOM 243 LT2 CLA X 1 -111.827 -93.233-235.435 1.00 0.00 A6
+ATOM 244 PX3 CLA X 1 151.180 99.388-340.613 1.00 0.00 A6
+ATOM 245 DT3 CLA X 1 224.588 19.480-265.860 1.00 0.00 A6
+ATOM 246 AK3 CLA X 1 251.607 27.627-146.926 1.00 0.00 A6
+ATOM 247 LT3 CLA X 1 217.550 57.864 -66.678 1.00 0.00 A6
+ATOM 248 HB0 CLA X 1 151.683 263.777-182.367 1.00 0.00 B6
+ATOM 249 PX1 CLA X 1 146.609 223.714-256.749 1.00 0.00 B6
+ATOM 250 DT1 CLA X 1 141.713 103.344-313.695 1.00 0.00 B6
+ATOM 251 AK1 CLA X 1 175.371 -0.848-262.690 1.00 0.00 B6
+ATOM 252 LT1 CLA X 1 188.241 -39.730-177.443 1.00 0.00 B6
+ATOM 253 PX2 CLA X 1 215.523 239.014-133.576 1.00 0.00 B6
+ATOM 254 DT2 CLA X 1 263.221 176.720 -21.125 1.00 0.00 B6
+ATOM 255 AK2 CLA X 1 218.030 156.206 95.151 1.00 0.00 B6
+ATOM 256 LT2 CLA X 1 140.536 148.285 145.576 1.00 0.00 B6
+ATOM 257 PX3 CLA X 1 83.654 306.316-155.002 1.00 0.00 B6
+ATOM 258 DT3 CLA X 1 -46.800 291.332-138.751 1.00 0.00 B6
+ATOM 259 AK3 CLA X 1 -116.444 204.434-186.863 1.00 0.00 B6
+ATOM 260 LT3 CLA X 1 -109.634 116.627-217.712 1.00 0.00 B6
+ATOM 261 HB0 CLA X 1 0.232 331.308 -93.118 1.00 0.00 C6
+ATOM 262 PX1 CLA X 1 -64.322 313.817-144.420 1.00 0.00 C6
+ATOM 263 DT1 CLA X 1 -106.786 228.382-232.998 1.00 0.00 C6
+ATOM 264 AK1 CLA X 1 -46.850 137.222-287.691 1.00 0.00 C6
+ATOM 265 LT1 CLA X 1 24.926 73.217-270.101 1.00 0.00 C6
+ATOM 266 PX2 CLA X 1 79.740 316.953-121.486 1.00 0.00 C6
+ATOM 267 DT2 CLA X 1 189.163 229.761-124.820 1.00 0.00 C6
+ATOM 268 AK2 CLA X 1 238.827 139.001 -50.135 1.00 0.00 C6
+ATOM 269 LT2 CLA X 1 218.915 77.201 18.776 1.00 0.00 C6
+ATOM 270 PX3 CLA X 1 -14.402 342.637 -11.493 1.00 0.00 C6
+ATOM 271 DT3 CLA X 1 -69.082 296.727 103.359 1.00 0.00 C6
+ATOM 272 AK3 CLA X 1 -146.495 205.240 144.395 1.00 0.00 C6
+ATOM 273 LT3 CLA X 1 -177.890 118.659 126.760 1.00 0.00 C6
+ATOM 274 HB0 CLA X 1 188.541 -1.488-331.473 1.00 0.00 A7
+ATOM 275 PX1 CLA X 1 251.234 12.306-275.579 1.00 0.00 A7
+ATOM 276 DT1 CLA X 1 280.592 69.705-159.192 1.00 0.00 A7
+ATOM 277 AK1 CLA X 1 218.091 155.028 -96.656 1.00 0.00 A7
+ATOM 278 LT1 CLA X 1 128.043 184.453 -85.497 1.00 0.00 A7
+ATOM 279 PX2 CLA X 1 140.484 65.324-352.917 1.00 0.00 A7
+ATOM 280 DT2 CLA X 1 23.007 135.296-333.137 1.00 0.00 A7
+ATOM 281 AK2 CLA X 1 -89.973 109.599-287.973 1.00 0.00 A7
+ATOM 282 LT2 CLA X 1 -136.656 50.229-235.435 1.00 0.00 A7
+ATOM 283 PX3 CLA X 1 161.662 -81.231-340.613 1.00 0.00 A7
+ATOM 284 DT3 CLA X 1 129.164-184.759-265.860 1.00 0.00 A7
+ATOM 285 AK3 CLA X 1 149.729-204.084-146.926 1.00 0.00 A7
+ATOM 286 LT3 CLA X 1 158.887-159.472 -66.678 1.00 0.00 A7
+ATOM 287 HB0 CLA X 1 304.279 0.528-182.367 1.00 0.00 B7
+ATOM 288 PX1 CLA X 1 267.047 -15.111-256.749 1.00 0.00 B7
+ATOM 289 DT1 CLA X 1 160.355 -71.055-313.695 1.00 0.00 B7
+ATOM 290 AK1 CLA X 1 86.951-152.300-262.690 1.00 0.00 B7
+ATOM 291 LT1 CLA X 1 59.713-182.886-177.443 1.00 0.00 B7
+ATOM 292 PX2 CLA X 1 314.754 -67.142-133.576 1.00 0.00 B7
+ATOM 293 DT2 CLA X 1 284.654-139.597 -21.125 1.00 0.00 B7
+ATOM 294 AK2 CLA X 1 244.294-110.717 95.151 1.00 0.00 B7
+ATOM 295 LT2 CLA X 1 198.687 -47.565 145.576 1.00 0.00 B7
+ATOM 296 PX3 CLA X 1 307.104 80.712-155.002 1.00 0.00 B7
+ATOM 297 DT3 CLA X 1 228.901 186.196-138.751 1.00 0.00 B7
+ATOM 298 AK3 CLA X 1 118.823 203.060-186.863 1.00 0.00 B7
+ATOM 299 LT3 CLA X 1 46.185 153.259-217.712 1.00 0.00 B7
+ATOM 300 HB0 CLA X 1 287.037 165.452 -93.118 1.00 0.00 C7
+ATOM 301 PX1 CLA X 1 239.613 212.613-144.420 1.00 0.00 C7
+ATOM 302 DT1 CLA X 1 144.392 206.670-232.998 1.00 0.00 C7
+ATOM 303 AK1 CLA X 1 95.413 109.184-287.691 1.00 0.00 C7
+ATOM 304 LT1 CLA X 1 75.871 15.022-270.101 1.00 0.00 C7
+ATOM 305 PX2 CLA X 1 314.360 89.420-121.486 1.00 0.00 C7
+ATOM 306 DT2 CLA X 1 293.560 -48.939-124.820 1.00 0.00 C7
+ATOM 307 AK2 CLA X 1 239.791-137.330 -50.135 1.00 0.00 C7
+ATOM 308 LT2 CLA X 1 176.315-150.986 18.776 1.00 0.00 C7
+ATOM 309 PX3 CLA X 1 289.532 183.791 -11.493 1.00 0.00 C7
+ATOM 310 DT3 CLA X 1 222.432 208.190 103.359 1.00 0.00 C7
+ATOM 311 AK3 CLA X 1 104.496 229.489 144.395 1.00 0.00 C7
+ATOM 312 LT3 CLA X 1 13.817 213.386 126.760 1.00 0.00 C7
+ATOM 313 HB0 CLA X 1 92.981-164.025-331.473 1.00 0.00 A8
+ATOM 314 PX1 CLA X 1 136.274-211.422-275.579 1.00 0.00 A8
+ATOM 315 DT1 CLA X 1 200.662-208.148-159.192 1.00 0.00 A8
+ATOM 316 AK1 CLA X 1 243.304-111.359 -96.656 1.00 0.00 A8
+ATOM 317 LT1 CLA X 1 223.763 -18.662 -85.497 1.00 0.00 A8
+ATOM 318 PX2 CLA X 1 126.815 -89.000-352.917 1.00 0.00 A8
+ATOM 319 DT2 CLA X 1 128.673 47.724-333.137 1.00 0.00 A8
+ATOM 320 AK2 CLA X 1 49.929 132.718-287.973 1.00 0.00 A8
+ATOM 321 LT2 CLA X 1 -24.828 143.462-235.435 1.00 0.00 A8
+ATOM 322 PX3 CLA X 1 10.483-180.619-340.613 1.00 0.00 A8
+ATOM 323 DT3 CLA X 1 -95.424-204.239-265.860 1.00 0.00 A8
+ATOM 324 AK3 CLA X 1 -101.877-231.712-146.926 1.00 0.00 A8
+ATOM 325 LT3 CLA X 1 -58.664-217.336 -66.678 1.00 0.00 A8
+ATOM 326 HB0 CLA X 1 152.597-263.250-182.367 1.00 0.00 B8
+ATOM 327 PX1 CLA X 1 120.437-238.824-256.749 1.00 0.00 B8
+ATOM 328 DT1 CLA X 1 18.642-174.399-313.695 1.00 0.00 B8
+ATOM 329 AK1 CLA X 1 -88.420-151.452-262.690 1.00 0.00 B8
+ATOM 330 LT1 CLA X 1 -128.527-143.156-177.443 1.00 0.00 B8
+ATOM 331 PX2 CLA X 1 99.230-306.155-133.576 1.00 0.00 B8
+ATOM 332 DT2 CLA X 1 21.433-316.316 -21.125 1.00 0.00 B8
+ATOM 333 AK2 CLA X 1 26.263-266.923 95.151 1.00 0.00 B8
+ATOM 334 LT2 CLA X 1 58.151-195.850 145.576 1.00 0.00 B8
+ATOM 335 PX3 CLA X 1 223.451-225.604-155.002 1.00 0.00 B8
+ATOM 336 DT3 CLA X 1 275.701-105.136-138.751 1.00 0.00 B8
+ATOM 337 AK3 CLA X 1 235.267 -1.374-186.863 1.00 0.00 B8
+ATOM 338 LT3 CLA X 1 155.819 36.632-217.712 1.00 0.00 B8
+ATOM 339 HB0 CLA X 1 286.805-165.855 -93.118 1.00 0.00 C8
+ATOM 340 PX1 CLA X 1 303.935-101.204-144.420 1.00 0.00 C8
+ATOM 341 DT1 CLA X 1 251.178 -21.712-232.998 1.00 0.00 C8
+ATOM 342 AK1 CLA X 1 142.263 -28.038-287.691 1.00 0.00 C8
+ATOM 343 LT1 CLA X 1 50.945 -58.195-270.101 1.00 0.00 C8
+ATOM 344 PX2 CLA X 1 234.620-227.534-121.486 1.00 0.00 C8
+ATOM 345 DT2 CLA X 1 104.398-278.700-124.820 1.00 0.00 C8
+ATOM 346 AK2 CLA X 1 0.965-276.330 -50.135 1.00 0.00 C8
+ATOM 347 LT2 CLA X 1 -42.600-228.187 18.776 1.00 0.00 C8
+ATOM 348 PX3 CLA X 1 303.934-158.846 -11.493 1.00 0.00 C8
+ATOM 349 DT3 CLA X 1 291.514 -88.537 103.359 1.00 0.00 C8
+ATOM 350 AK3 CLA X 1 250.991 24.248 144.395 1.00 0.00 C8
+ATOM 351 LT3 CLA X 1 191.706 94.728 126.760 1.00 0.00 C8
+ATOM 352 HB0 CLA X 1 -95.559-162.537-331.473 1.00 0.00 A9
+ATOM 353 PX1 CLA X 1 -114.959-223.728-275.579 1.00 0.00 A9
+ATOM 354 DT1 CLA X 1 -79.930-277.853-159.192 1.00 0.00 A9
+ATOM 355 AK1 CLA X 1 25.213-266.386 -96.656 1.00 0.00 A9
+ATOM 356 LT1 CLA X 1 95.719-203.115 -85.497 1.00 0.00 A9
+ATOM 357 PX2 CLA X 1 -13.669-154.325-352.917 1.00 0.00 A9
+ATOM 358 DT2 CLA X 1 105.666 -87.572-333.137 1.00 0.00 A9
+ATOM 359 AK2 CLA X 1 139.902 23.120-287.973 1.00 0.00 A9
+ATOM 360 LT2 CLA X 1 111.827 93.233-235.435 1.00 0.00 A9
+ATOM 361 PX3 CLA X 1 -151.180 -99.388-340.613 1.00 0.00 A9
+ATOM 362 DT3 CLA X 1 -224.588 -19.480-265.860 1.00 0.00 A9
+ATOM 363 AK3 CLA X 1 -251.607 -27.627-146.926 1.00 0.00 A9
+ATOM 364 LT3 CLA X 1 -217.550 -57.864 -66.678 1.00 0.00 A9
+ATOM 365 HB0 CLA X 1 -151.683-263.777-182.367 1.00 0.00 B9
+ATOM 366 PX1 CLA X 1 -146.609-223.714-256.749 1.00 0.00 B9
+ATOM 367 DT1 CLA X 1 -141.713-103.344-313.695 1.00 0.00 B9
+ATOM 368 AK1 CLA X 1 -175.371 0.848-262.690 1.00 0.00 B9
+ATOM 369 LT1 CLA X 1 -188.241 39.730-177.443 1.00 0.00 B9
+ATOM 370 PX2 CLA X 1 -215.523-239.014-133.576 1.00 0.00 B9
+ATOM 371 DT2 CLA X 1 -263.221-176.720 -21.125 1.00 0.00 B9
+ATOM 372 AK2 CLA X 1 -218.030-156.206 95.151 1.00 0.00 B9
+ATOM 373 LT2 CLA X 1 -140.536-148.285 145.576 1.00 0.00 B9
+ATOM 374 PX3 CLA X 1 -83.654-306.316-155.002 1.00 0.00 B9
+ATOM 375 DT3 CLA X 1 46.800-291.332-138.751 1.00 0.00 B9
+ATOM 376 AK3 CLA X 1 116.444-204.434-186.863 1.00 0.00 B9
+ATOM 377 LT3 CLA X 1 109.634-116.627-217.712 1.00 0.00 B9
+ATOM 378 HB0 CLA X 1 -0.232-331.308 -93.118 1.00 0.00 C9
+ATOM 379 PX1 CLA X 1 64.322-313.817-144.420 1.00 0.00 C9
+ATOM 380 DT1 CLA X 1 106.786-228.382-232.998 1.00 0.00 C9
+ATOM 381 AK1 CLA X 1 46.850-137.222-287.691 1.00 0.00 C9
+ATOM 382 LT1 CLA X 1 -24.926 -73.217-270.101 1.00 0.00 C9
+ATOM 383 PX2 CLA X 1 -79.740-316.953-121.486 1.00 0.00 C9
+ATOM 384 DT2 CLA X 1 -189.163-229.761-124.820 1.00 0.00 C9
+ATOM 385 AK2 CLA X 1 -238.827-139.001 -50.135 1.00 0.00 C9
+ATOM 386 LT2 CLA X 1 -218.915 -77.201 18.776 1.00 0.00 C9
+ATOM 387 PX3 CLA X 1 14.402-342.637 -11.493 1.00 0.00 C9
+ATOM 388 DT3 CLA X 1 69.082-296.727 103.359 1.00 0.00 C9
+ATOM 389 AK3 CLA X 1 146.495-205.240 144.395 1.00 0.00 C9
+ATOM 390 LT3 CLA X 1 177.890-118.659 126.760 1.00 0.00 C9
+ATOM 391 HB0 CLA X 1 -188.541 1.488-331.473 1.00 0.00 A10
+ATOM 392 PX1 CLA X 1 -251.234 -12.306-275.579 1.00 0.00 A10
+ATOM 393 DT1 CLA X 1 -280.592 -69.705-159.192 1.00 0.00 A10
+ATOM 394 AK1 CLA X 1 -218.091-155.028 -96.656 1.00 0.00 A10
+ATOM 395 LT1 CLA X 1 -128.043-184.453 -85.497 1.00 0.00 A10
+ATOM 396 PX2 CLA X 1 -140.484 -65.324-352.917 1.00 0.00 A10
+ATOM 397 DT2 CLA X 1 -23.007-135.296-333.137 1.00 0.00 A10
+ATOM 398 AK2 CLA X 1 89.973-109.599-287.973 1.00 0.00 A10
+ATOM 399 LT2 CLA X 1 136.656 -50.229-235.435 1.00 0.00 A10
+ATOM 400 PX3 CLA X 1 -161.662 81.231-340.613 1.00 0.00 A10
+ATOM 401 DT3 CLA X 1 -129.164 184.759-265.860 1.00 0.00 A10
+ATOM 402 AK3 CLA X 1 -149.729 204.084-146.926 1.00 0.00 A10
+ATOM 403 LT3 CLA X 1 -158.887 159.472 -66.678 1.00 0.00 A10
+ATOM 404 HB0 CLA X 1 -304.279 -0.528-182.367 1.00 0.00 B10
+ATOM 405 PX1 CLA X 1 -267.047 15.111-256.749 1.00 0.00 B10
+ATOM 406 DT1 CLA X 1 -160.355 71.055-313.695 1.00 0.00 B10
+ATOM 407 AK1 CLA X 1 -86.951 152.300-262.690 1.00 0.00 B10
+ATOM 408 LT1 CLA X 1 -59.713 182.886-177.443 1.00 0.00 B10
+ATOM 409 PX2 CLA X 1 -314.754 67.142-133.576 1.00 0.00 B10
+ATOM 410 DT2 CLA X 1 -284.654 139.597 -21.125 1.00 0.00 B10
+ATOM 411 AK2 CLA X 1 -244.294 110.717 95.151 1.00 0.00 B10
+ATOM 412 LT2 CLA X 1 -198.687 47.565 145.576 1.00 0.00 B10
+ATOM 413 PX3 CLA X 1 -307.104 -80.712-155.002 1.00 0.00 B10
+ATOM 414 DT3 CLA X 1 -228.901-186.196-138.751 1.00 0.00 B10
+ATOM 415 AK3 CLA X 1 -118.823-203.060-186.863 1.00 0.00 B10
+ATOM 416 LT3 CLA X 1 -46.185-153.259-217.712 1.00 0.00 B10
+ATOM 417 HB0 CLA X 1 -287.037-165.452 -93.118 1.00 0.00 C10
+ATOM 418 PX1 CLA X 1 -239.613-212.613-144.420 1.00 0.00 C10
+ATOM 419 DT1 CLA X 1 -144.392-206.670-232.998 1.00 0.00 C10
+ATOM 420 AK1 CLA X 1 -95.413-109.184-287.691 1.00 0.00 C10
+ATOM 421 LT1 CLA X 1 -75.871 -15.022-270.101 1.00 0.00 C10
+ATOM 422 PX2 CLA X 1 -314.360 -89.420-121.486 1.00 0.00 C10
+ATOM 423 DT2 CLA X 1 -293.560 48.939-124.820 1.00 0.00 C10
+ATOM 424 AK2 CLA X 1 -239.791 137.330 -50.135 1.00 0.00 C10
+ATOM 425 LT2 CLA X 1 -176.315 150.986 18.776 1.00 0.00 C10
+ATOM 426 PX3 CLA X 1 -289.532-183.791 -11.493 1.00 0.00 C10
+ATOM 427 DT3 CLA X 1 -222.432-208.190 103.359 1.00 0.00 C10
+ATOM 428 AK3 CLA X 1 -104.496-229.489 144.395 1.00 0.00 C10
+ATOM 429 LT3 CLA X 1 -13.817-213.386 126.760 1.00 0.00 C10
+ATOM 430 HB0 CLA X 1 -92.981 164.025-331.473 1.00 0.00 A11
+ATOM 431 PX1 CLA X 1 -136.274 211.422-275.579 1.00 0.00 A11
+ATOM 432 DT1 CLA X 1 -200.662 208.148-159.192 1.00 0.00 A11
+ATOM 433 AK1 CLA X 1 -243.304 111.359 -96.656 1.00 0.00 A11
+ATOM 434 LT1 CLA X 1 -223.763 18.662 -85.497 1.00 0.00 A11
+ATOM 435 PX2 CLA X 1 -126.815 89.000-352.917 1.00 0.00 A11
+ATOM 436 DT2 CLA X 1 -128.673 -47.724-333.137 1.00 0.00 A11
+ATOM 437 AK2 CLA X 1 -49.929-132.718-287.973 1.00 0.00 A11
+ATOM 438 LT2 CLA X 1 24.828-143.462-235.435 1.00 0.00 A11
+ATOM 439 PX3 CLA X 1 -10.483 180.619-340.613 1.00 0.00 A11
+ATOM 440 DT3 CLA X 1 95.424 204.239-265.860 1.00 0.00 A11
+ATOM 441 AK3 CLA X 1 101.877 231.712-146.926 1.00 0.00 A11
+ATOM 442 LT3 CLA X 1 58.664 217.336 -66.678 1.00 0.00 A11
+ATOM 443 HB0 CLA X 1 -152.597 263.250-182.367 1.00 0.00 B11
+ATOM 444 PX1 CLA X 1 -120.437 238.824-256.749 1.00 0.00 B11
+ATOM 445 DT1 CLA X 1 -18.642 174.399-313.695 1.00 0.00 B11
+ATOM 446 AK1 CLA X 1 88.420 151.452-262.690 1.00 0.00 B11
+ATOM 447 LT1 CLA X 1 128.527 143.156-177.443 1.00 0.00 B11
+ATOM 448 PX2 CLA X 1 -99.230 306.155-133.576 1.00 0.00 B11
+ATOM 449 DT2 CLA X 1 -21.433 316.316 -21.125 1.00 0.00 B11
+ATOM 450 AK2 CLA X 1 -26.263 266.923 95.151 1.00 0.00 B11
+ATOM 451 LT2 CLA X 1 -58.151 195.850 145.576 1.00 0.00 B11
+ATOM 452 PX3 CLA X 1 -223.451 225.604-155.002 1.00 0.00 B11
+ATOM 453 DT3 CLA X 1 -275.701 105.136-138.751 1.00 0.00 B11
+ATOM 454 AK3 CLA X 1 -235.267 1.374-186.863 1.00 0.00 B11
+ATOM 455 LT3 CLA X 1 -155.819 -36.632-217.712 1.00 0.00 B11
+ATOM 456 HB0 CLA X 1 -286.805 165.855 -93.118 1.00 0.00 C11
+ATOM 457 PX1 CLA X 1 -303.935 101.204-144.420 1.00 0.00 C11
+ATOM 458 DT1 CLA X 1 -251.178 21.712-232.998 1.00 0.00 C11
+ATOM 459 AK1 CLA X 1 -142.263 28.038-287.691 1.00 0.00 C11
+ATOM 460 LT1 CLA X 1 -50.945 58.195-270.101 1.00 0.00 C11
+ATOM 461 PX2 CLA X 1 -234.620 227.534-121.486 1.00 0.00 C11
+ATOM 462 DT2 CLA X 1 -104.398 278.700-124.820 1.00 0.00 C11
+ATOM 463 AK2 CLA X 1 -0.965 276.330 -50.135 1.00 0.00 C11
+ATOM 464 LT2 CLA X 1 42.600 228.187 18.776 1.00 0.00 C11
+ATOM 465 PX3 CLA X 1 -303.934 158.846 -11.493 1.00 0.00 C11
+ATOM 466 DT3 CLA X 1 -291.514 88.537 103.359 1.00 0.00 C11
+ATOM 467 AK3 CLA X 1 -250.991 -24.248 144.395 1.00 0.00 C11
+ATOM 468 LT3 CLA X 1 -191.706 -94.728 126.760 1.00 0.00 C11
+END
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.pdb
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,1078 @@
+PSF
+
+ 38 !NTITLE
+ REMARKS original generated structure x-plor psf file
+ REMARKS topology top_cg_clath.impr.inp
+ REMARKS segment A0 { first NONE; last NONE; auto angles }
+ REMARKS segment B0 { first NONE; last NONE; auto angles }
+ REMARKS segment C0 { first NONE; last NONE; auto angles }
+ REMARKS segment A1 { first NONE; last NONE; auto angles }
+ REMARKS segment B1 { first NONE; last NONE; auto angles }
+ REMARKS segment C1 { first NONE; last NONE; auto angles }
+ REMARKS segment A2 { first NONE; last NONE; auto angles }
+ REMARKS segment B2 { first NONE; last NONE; auto angles }
+ REMARKS segment C2 { first NONE; last NONE; auto angles }
+ REMARKS segment A3 { first NONE; last NONE; auto angles }
+ REMARKS segment B3 { first NONE; last NONE; auto angles }
+ REMARKS segment C3 { first NONE; last NONE; auto angles }
+ REMARKS segment A4 { first NONE; last NONE; auto angles }
+ REMARKS segment B4 { first NONE; last NONE; auto angles }
+ REMARKS segment C4 { first NONE; last NONE; auto angles }
+ REMARKS segment A5 { first NONE; last NONE; auto angles }
+ REMARKS segment B5 { first NONE; last NONE; auto angles }
+ REMARKS segment C5 { first NONE; last NONE; auto angles }
+ REMARKS segment A6 { first NONE; last NONE; auto angles }
+ REMARKS segment B6 { first NONE; last NONE; auto angles }
+ REMARKS segment C6 { first NONE; last NONE; auto angles }
+ REMARKS segment A7 { first NONE; last NONE; auto angles }
+ REMARKS segment B7 { first NONE; last NONE; auto angles }
+ REMARKS segment C7 { first NONE; last NONE; auto angles }
+ REMARKS segment A8 { first NONE; last NONE; auto angles }
+ REMARKS segment B8 { first NONE; last NONE; auto angles }
+ REMARKS segment C8 { first NONE; last NONE; auto angles }
+ REMARKS segment A9 { first NONE; last NONE; auto angles }
+ REMARKS segment B9 { first NONE; last NONE; auto angles }
+ REMARKS segment C9 { first NONE; last NONE; auto angles }
+ REMARKS segment A10 { first NONE; last NONE; auto angles }
+ REMARKS segment B10 { first NONE; last NONE; auto angles }
+ REMARKS segment C10 { first NONE; last NONE; auto angles }
+ REMARKS segment A11 { first NONE; last NONE; auto angles }
+ REMARKS segment B11 { first NONE; last NONE; auto angles }
+ REMARKS segment C11 { first NONE; last NONE; auto angles }
+
+ 468 !NATOM
+ 1 A0 1 CLA HB0 HB 0.000000 30478.0300 0
+ 2 A0 1 CLA PX1 PX 0.000000 46422.2000 0
+ 3 A0 1 CLA DT1 DT 0.000000 49195.2000 0
+ 4 A0 1 CLA AK1 AK 0.000000 34620.7800 0
+ 5 A0 1 CLA LT1 LT 0.000000 55013.7800 0
+ 6 A0 1 CLA PX2 PX 0.000000 46422.2000 0
+ 7 A0 1 CLA DT2 DT 0.000000 49195.2000 0
+ 8 A0 1 CLA AK2 AK 0.000000 34620.7800 0
+ 9 A0 1 CLA LT2 LT 0.000000 55013.7800 0
+ 10 A0 1 CLA PX3 PX 0.000000 46422.2000 0
+ 11 A0 1 CLA DT3 DT 0.000000 49195.2000 0
+ 12 A0 1 CLA AK3 AK 0.000000 34620.7800 0
+ 13 A0 1 CLA LT3 LT 0.000000 55013.7800 0
+ 14 B0 1 CLA HB0 HB 0.000000 30478.0300 0
+ 15 B0 1 CLA PX1 PX 0.000000 46422.2000 0
+ 16 B0 1 CLA DT1 DT 0.000000 49195.2000 0
+ 17 B0 1 CLA AK1 AK 0.000000 34620.7800 0
+ 18 B0 1 CLA LT1 LT 0.000000 55013.7800 0
+ 19 B0 1 CLA PX2 PX 0.000000 46422.2000 0
+ 20 B0 1 CLA DT2 DT 0.000000 49195.2000 0
+ 21 B0 1 CLA AK2 AK 0.000000 34620.7800 0
+ 22 B0 1 CLA LT2 LT 0.000000 55013.7800 0
+ 23 B0 1 CLA PX3 PX 0.000000 46422.2000 0
+ 24 B0 1 CLA DT3 DT 0.000000 49195.2000 0
+ 25 B0 1 CLA AK3 AK 0.000000 34620.7800 0
+ 26 B0 1 CLA LT3 LT 0.000000 55013.7800 0
+ 27 C0 1 CLA HB0 HB 0.000000 30478.0300 0
+ 28 C0 1 CLA PX1 PX 0.000000 46422.2000 0
+ 29 C0 1 CLA DT1 DT 0.000000 49195.2000 0
+ 30 C0 1 CLA AK1 AK 0.000000 34620.7800 0
+ 31 C0 1 CLA LT1 LT 0.000000 55013.7800 0
+ 32 C0 1 CLA PX2 PX 0.000000 46422.2000 0
+ 33 C0 1 CLA DT2 DT 0.000000 49195.2000 0
+ 34 C0 1 CLA AK2 AK 0.000000 34620.7800 0
+ 35 C0 1 CLA LT2 LT 0.000000 55013.7800 0
+ 36 C0 1 CLA PX3 PX 0.000000 46422.2000 0
+ 37 C0 1 CLA DT3 DT 0.000000 49195.2000 0
+ 38 C0 1 CLA AK3 AK 0.000000 34620.7800 0
+ 39 C0 1 CLA LT3 LT 0.000000 55013.7800 0
+ 40 A1 1 CLA HB0 HB 0.000000 30478.0300 0
+ 41 A1 1 CLA PX1 PX 0.000000 46422.2000 0
+ 42 A1 1 CLA DT1 DT 0.000000 49195.2000 0
+ 43 A1 1 CLA AK1 AK 0.000000 34620.7800 0
+ 44 A1 1 CLA LT1 LT 0.000000 55013.7800 0
+ 45 A1 1 CLA PX2 PX 0.000000 46422.2000 0
+ 46 A1 1 CLA DT2 DT 0.000000 49195.2000 0
+ 47 A1 1 CLA AK2 AK 0.000000 34620.7800 0
+ 48 A1 1 CLA LT2 LT 0.000000 55013.7800 0
+ 49 A1 1 CLA PX3 PX 0.000000 46422.2000 0
+ 50 A1 1 CLA DT3 DT 0.000000 49195.2000 0
+ 51 A1 1 CLA AK3 AK 0.000000 34620.7800 0
+ 52 A1 1 CLA LT3 LT 0.000000 55013.7800 0
+ 53 B1 1 CLA HB0 HB 0.000000 30478.0300 0
+ 54 B1 1 CLA PX1 PX 0.000000 46422.2000 0
+ 55 B1 1 CLA DT1 DT 0.000000 49195.2000 0
+ 56 B1 1 CLA AK1 AK 0.000000 34620.7800 0
+ 57 B1 1 CLA LT1 LT 0.000000 55013.7800 0
+ 58 B1 1 CLA PX2 PX 0.000000 46422.2000 0
+ 59 B1 1 CLA DT2 DT 0.000000 49195.2000 0
+ 60 B1 1 CLA AK2 AK 0.000000 34620.7800 0
+ 61 B1 1 CLA LT2 LT 0.000000 55013.7800 0
+ 62 B1 1 CLA PX3 PX 0.000000 46422.2000 0
+ 63 B1 1 CLA DT3 DT 0.000000 49195.2000 0
+ 64 B1 1 CLA AK3 AK 0.000000 34620.7800 0
+ 65 B1 1 CLA LT3 LT 0.000000 55013.7800 0
+ 66 C1 1 CLA HB0 HB 0.000000 30478.0300 0
+ 67 C1 1 CLA PX1 PX 0.000000 46422.2000 0
+ 68 C1 1 CLA DT1 DT 0.000000 49195.2000 0
+ 69 C1 1 CLA AK1 AK 0.000000 34620.7800 0
+ 70 C1 1 CLA LT1 LT 0.000000 55013.7800 0
+ 71 C1 1 CLA PX2 PX 0.000000 46422.2000 0
+ 72 C1 1 CLA DT2 DT 0.000000 49195.2000 0
+ 73 C1 1 CLA AK2 AK 0.000000 34620.7800 0
+ 74 C1 1 CLA LT2 LT 0.000000 55013.7800 0
+ 75 C1 1 CLA PX3 PX 0.000000 46422.2000 0
+ 76 C1 1 CLA DT3 DT 0.000000 49195.2000 0
+ 77 C1 1 CLA AK3 AK 0.000000 34620.7800 0
+ 78 C1 1 CLA LT3 LT 0.000000 55013.7800 0
+ 79 A2 1 CLA HB0 HB 0.000000 30478.0300 0
+ 80 A2 1 CLA PX1 PX 0.000000 46422.2000 0
+ 81 A2 1 CLA DT1 DT 0.000000 49195.2000 0
+ 82 A2 1 CLA AK1 AK 0.000000 34620.7800 0
+ 83 A2 1 CLA LT1 LT 0.000000 55013.7800 0
+ 84 A2 1 CLA PX2 PX 0.000000 46422.2000 0
+ 85 A2 1 CLA DT2 DT 0.000000 49195.2000 0
+ 86 A2 1 CLA AK2 AK 0.000000 34620.7800 0
+ 87 A2 1 CLA LT2 LT 0.000000 55013.7800 0
+ 88 A2 1 CLA PX3 PX 0.000000 46422.2000 0
+ 89 A2 1 CLA DT3 DT 0.000000 49195.2000 0
+ 90 A2 1 CLA AK3 AK 0.000000 34620.7800 0
+ 91 A2 1 CLA LT3 LT 0.000000 55013.7800 0
+ 92 B2 1 CLA HB0 HB 0.000000 30478.0300 0
+ 93 B2 1 CLA PX1 PX 0.000000 46422.2000 0
+ 94 B2 1 CLA DT1 DT 0.000000 49195.2000 0
+ 95 B2 1 CLA AK1 AK 0.000000 34620.7800 0
+ 96 B2 1 CLA LT1 LT 0.000000 55013.7800 0
+ 97 B2 1 CLA PX2 PX 0.000000 46422.2000 0
+ 98 B2 1 CLA DT2 DT 0.000000 49195.2000 0
+ 99 B2 1 CLA AK2 AK 0.000000 34620.7800 0
+ 100 B2 1 CLA LT2 LT 0.000000 55013.7800 0
+ 101 B2 1 CLA PX3 PX 0.000000 46422.2000 0
+ 102 B2 1 CLA DT3 DT 0.000000 49195.2000 0
+ 103 B2 1 CLA AK3 AK 0.000000 34620.7800 0
+ 104 B2 1 CLA LT3 LT 0.000000 55013.7800 0
+ 105 C2 1 CLA HB0 HB 0.000000 30478.0300 0
+ 106 C2 1 CLA PX1 PX 0.000000 46422.2000 0
+ 107 C2 1 CLA DT1 DT 0.000000 49195.2000 0
+ 108 C2 1 CLA AK1 AK 0.000000 34620.7800 0
+ 109 C2 1 CLA LT1 LT 0.000000 55013.7800 0
+ 110 C2 1 CLA PX2 PX 0.000000 46422.2000 0
+ 111 C2 1 CLA DT2 DT 0.000000 49195.2000 0
+ 112 C2 1 CLA AK2 AK 0.000000 34620.7800 0
+ 113 C2 1 CLA LT2 LT 0.000000 55013.7800 0
+ 114 C2 1 CLA PX3 PX 0.000000 46422.2000 0
+ 115 C2 1 CLA DT3 DT 0.000000 49195.2000 0
+ 116 C2 1 CLA AK3 AK 0.000000 34620.7800 0
+ 117 C2 1 CLA LT3 LT 0.000000 55013.7800 0
+ 118 A3 1 CLA HB0 HB 0.000000 30478.0300 0
+ 119 A3 1 CLA PX1 PX 0.000000 46422.2000 0
+ 120 A3 1 CLA DT1 DT 0.000000 49195.2000 0
+ 121 A3 1 CLA AK1 AK 0.000000 34620.7800 0
+ 122 A3 1 CLA LT1 LT 0.000000 55013.7800 0
+ 123 A3 1 CLA PX2 PX 0.000000 46422.2000 0
+ 124 A3 1 CLA DT2 DT 0.000000 49195.2000 0
+ 125 A3 1 CLA AK2 AK 0.000000 34620.7800 0
+ 126 A3 1 CLA LT2 LT 0.000000 55013.7800 0
+ 127 A3 1 CLA PX3 PX 0.000000 46422.2000 0
+ 128 A3 1 CLA DT3 DT 0.000000 49195.2000 0
+ 129 A3 1 CLA AK3 AK 0.000000 34620.7800 0
+ 130 A3 1 CLA LT3 LT 0.000000 55013.7800 0
+ 131 B3 1 CLA HB0 HB 0.000000 30478.0300 0
+ 132 B3 1 CLA PX1 PX 0.000000 46422.2000 0
+ 133 B3 1 CLA DT1 DT 0.000000 49195.2000 0
+ 134 B3 1 CLA AK1 AK 0.000000 34620.7800 0
+ 135 B3 1 CLA LT1 LT 0.000000 55013.7800 0
+ 136 B3 1 CLA PX2 PX 0.000000 46422.2000 0
+ 137 B3 1 CLA DT2 DT 0.000000 49195.2000 0
+ 138 B3 1 CLA AK2 AK 0.000000 34620.7800 0
+ 139 B3 1 CLA LT2 LT 0.000000 55013.7800 0
+ 140 B3 1 CLA PX3 PX 0.000000 46422.2000 0
+ 141 B3 1 CLA DT3 DT 0.000000 49195.2000 0
+ 142 B3 1 CLA AK3 AK 0.000000 34620.7800 0
+ 143 B3 1 CLA LT3 LT 0.000000 55013.7800 0
+ 144 C3 1 CLA HB0 HB 0.000000 30478.0300 0
+ 145 C3 1 CLA PX1 PX 0.000000 46422.2000 0
+ 146 C3 1 CLA DT1 DT 0.000000 49195.2000 0
+ 147 C3 1 CLA AK1 AK 0.000000 34620.7800 0
+ 148 C3 1 CLA LT1 LT 0.000000 55013.7800 0
+ 149 C3 1 CLA PX2 PX 0.000000 46422.2000 0
+ 150 C3 1 CLA DT2 DT 0.000000 49195.2000 0
+ 151 C3 1 CLA AK2 AK 0.000000 34620.7800 0
+ 152 C3 1 CLA LT2 LT 0.000000 55013.7800 0
+ 153 C3 1 CLA PX3 PX 0.000000 46422.2000 0
+ 154 C3 1 CLA DT3 DT 0.000000 49195.2000 0
+ 155 C3 1 CLA AK3 AK 0.000000 34620.7800 0
+ 156 C3 1 CLA LT3 LT 0.000000 55013.7800 0
+ 157 A4 1 CLA HB0 HB 0.000000 30478.0300 0
+ 158 A4 1 CLA PX1 PX 0.000000 46422.2000 0
+ 159 A4 1 CLA DT1 DT 0.000000 49195.2000 0
+ 160 A4 1 CLA AK1 AK 0.000000 34620.7800 0
+ 161 A4 1 CLA LT1 LT 0.000000 55013.7800 0
+ 162 A4 1 CLA PX2 PX 0.000000 46422.2000 0
+ 163 A4 1 CLA DT2 DT 0.000000 49195.2000 0
+ 164 A4 1 CLA AK2 AK 0.000000 34620.7800 0
+ 165 A4 1 CLA LT2 LT 0.000000 55013.7800 0
+ 166 A4 1 CLA PX3 PX 0.000000 46422.2000 0
+ 167 A4 1 CLA DT3 DT 0.000000 49195.2000 0
+ 168 A4 1 CLA AK3 AK 0.000000 34620.7800 0
+ 169 A4 1 CLA LT3 LT 0.000000 55013.7800 0
+ 170 B4 1 CLA HB0 HB 0.000000 30478.0300 0
+ 171 B4 1 CLA PX1 PX 0.000000 46422.2000 0
+ 172 B4 1 CLA DT1 DT 0.000000 49195.2000 0
+ 173 B4 1 CLA AK1 AK 0.000000 34620.7800 0
+ 174 B4 1 CLA LT1 LT 0.000000 55013.7800 0
+ 175 B4 1 CLA PX2 PX 0.000000 46422.2000 0
+ 176 B4 1 CLA DT2 DT 0.000000 49195.2000 0
+ 177 B4 1 CLA AK2 AK 0.000000 34620.7800 0
+ 178 B4 1 CLA LT2 LT 0.000000 55013.7800 0
+ 179 B4 1 CLA PX3 PX 0.000000 46422.2000 0
+ 180 B4 1 CLA DT3 DT 0.000000 49195.2000 0
+ 181 B4 1 CLA AK3 AK 0.000000 34620.7800 0
+ 182 B4 1 CLA LT3 LT 0.000000 55013.7800 0
+ 183 C4 1 CLA HB0 HB 0.000000 30478.0300 0
+ 184 C4 1 CLA PX1 PX 0.000000 46422.2000 0
+ 185 C4 1 CLA DT1 DT 0.000000 49195.2000 0
+ 186 C4 1 CLA AK1 AK 0.000000 34620.7800 0
+ 187 C4 1 CLA LT1 LT 0.000000 55013.7800 0
+ 188 C4 1 CLA PX2 PX 0.000000 46422.2000 0
+ 189 C4 1 CLA DT2 DT 0.000000 49195.2000 0
+ 190 C4 1 CLA AK2 AK 0.000000 34620.7800 0
+ 191 C4 1 CLA LT2 LT 0.000000 55013.7800 0
+ 192 C4 1 CLA PX3 PX 0.000000 46422.2000 0
+ 193 C4 1 CLA DT3 DT 0.000000 49195.2000 0
+ 194 C4 1 CLA AK3 AK 0.000000 34620.7800 0
+ 195 C4 1 CLA LT3 LT 0.000000 55013.7800 0
+ 196 A5 1 CLA HB0 HB 0.000000 30478.0300 0
+ 197 A5 1 CLA PX1 PX 0.000000 46422.2000 0
+ 198 A5 1 CLA DT1 DT 0.000000 49195.2000 0
+ 199 A5 1 CLA AK1 AK 0.000000 34620.7800 0
+ 200 A5 1 CLA LT1 LT 0.000000 55013.7800 0
+ 201 A5 1 CLA PX2 PX 0.000000 46422.2000 0
+ 202 A5 1 CLA DT2 DT 0.000000 49195.2000 0
+ 203 A5 1 CLA AK2 AK 0.000000 34620.7800 0
+ 204 A5 1 CLA LT2 LT 0.000000 55013.7800 0
+ 205 A5 1 CLA PX3 PX 0.000000 46422.2000 0
+ 206 A5 1 CLA DT3 DT 0.000000 49195.2000 0
+ 207 A5 1 CLA AK3 AK 0.000000 34620.7800 0
+ 208 A5 1 CLA LT3 LT 0.000000 55013.7800 0
+ 209 B5 1 CLA HB0 HB 0.000000 30478.0300 0
+ 210 B5 1 CLA PX1 PX 0.000000 46422.2000 0
+ 211 B5 1 CLA DT1 DT 0.000000 49195.2000 0
+ 212 B5 1 CLA AK1 AK 0.000000 34620.7800 0
+ 213 B5 1 CLA LT1 LT 0.000000 55013.7800 0
+ 214 B5 1 CLA PX2 PX 0.000000 46422.2000 0
+ 215 B5 1 CLA DT2 DT 0.000000 49195.2000 0
+ 216 B5 1 CLA AK2 AK 0.000000 34620.7800 0
+ 217 B5 1 CLA LT2 LT 0.000000 55013.7800 0
+ 218 B5 1 CLA PX3 PX 0.000000 46422.2000 0
+ 219 B5 1 CLA DT3 DT 0.000000 49195.2000 0
+ 220 B5 1 CLA AK3 AK 0.000000 34620.7800 0
+ 221 B5 1 CLA LT3 LT 0.000000 55013.7800 0
+ 222 C5 1 CLA HB0 HB 0.000000 30478.0300 0
+ 223 C5 1 CLA PX1 PX 0.000000 46422.2000 0
+ 224 C5 1 CLA DT1 DT 0.000000 49195.2000 0
+ 225 C5 1 CLA AK1 AK 0.000000 34620.7800 0
+ 226 C5 1 CLA LT1 LT 0.000000 55013.7800 0
+ 227 C5 1 CLA PX2 PX 0.000000 46422.2000 0
+ 228 C5 1 CLA DT2 DT 0.000000 49195.2000 0
+ 229 C5 1 CLA AK2 AK 0.000000 34620.7800 0
+ 230 C5 1 CLA LT2 LT 0.000000 55013.7800 0
+ 231 C5 1 CLA PX3 PX 0.000000 46422.2000 0
+ 232 C5 1 CLA DT3 DT 0.000000 49195.2000 0
+ 233 C5 1 CLA AK3 AK 0.000000 34620.7800 0
+ 234 C5 1 CLA LT3 LT 0.000000 55013.7800 0
+ 235 A6 1 CLA HB0 HB 0.000000 30478.0300 0
+ 236 A6 1 CLA PX1 PX 0.000000 46422.2000 0
+ 237 A6 1 CLA DT1 DT 0.000000 49195.2000 0
+ 238 A6 1 CLA AK1 AK 0.000000 34620.7800 0
+ 239 A6 1 CLA LT1 LT 0.000000 55013.7800 0
+ 240 A6 1 CLA PX2 PX 0.000000 46422.2000 0
+ 241 A6 1 CLA DT2 DT 0.000000 49195.2000 0
+ 242 A6 1 CLA AK2 AK 0.000000 34620.7800 0
+ 243 A6 1 CLA LT2 LT 0.000000 55013.7800 0
+ 244 A6 1 CLA PX3 PX 0.000000 46422.2000 0
+ 245 A6 1 CLA DT3 DT 0.000000 49195.2000 0
+ 246 A6 1 CLA AK3 AK 0.000000 34620.7800 0
+ 247 A6 1 CLA LT3 LT 0.000000 55013.7800 0
+ 248 B6 1 CLA HB0 HB 0.000000 30478.0300 0
+ 249 B6 1 CLA PX1 PX 0.000000 46422.2000 0
+ 250 B6 1 CLA DT1 DT 0.000000 49195.2000 0
+ 251 B6 1 CLA AK1 AK 0.000000 34620.7800 0
+ 252 B6 1 CLA LT1 LT 0.000000 55013.7800 0
+ 253 B6 1 CLA PX2 PX 0.000000 46422.2000 0
+ 254 B6 1 CLA DT2 DT 0.000000 49195.2000 0
+ 255 B6 1 CLA AK2 AK 0.000000 34620.7800 0
+ 256 B6 1 CLA LT2 LT 0.000000 55013.7800 0
+ 257 B6 1 CLA PX3 PX 0.000000 46422.2000 0
+ 258 B6 1 CLA DT3 DT 0.000000 49195.2000 0
+ 259 B6 1 CLA AK3 AK 0.000000 34620.7800 0
+ 260 B6 1 CLA LT3 LT 0.000000 55013.7800 0
+ 261 C6 1 CLA HB0 HB 0.000000 30478.0300 0
+ 262 C6 1 CLA PX1 PX 0.000000 46422.2000 0
+ 263 C6 1 CLA DT1 DT 0.000000 49195.2000 0
+ 264 C6 1 CLA AK1 AK 0.000000 34620.7800 0
+ 265 C6 1 CLA LT1 LT 0.000000 55013.7800 0
+ 266 C6 1 CLA PX2 PX 0.000000 46422.2000 0
+ 267 C6 1 CLA DT2 DT 0.000000 49195.2000 0
+ 268 C6 1 CLA AK2 AK 0.000000 34620.7800 0
+ 269 C6 1 CLA LT2 LT 0.000000 55013.7800 0
+ 270 C6 1 CLA PX3 PX 0.000000 46422.2000 0
+ 271 C6 1 CLA DT3 DT 0.000000 49195.2000 0
+ 272 C6 1 CLA AK3 AK 0.000000 34620.7800 0
+ 273 C6 1 CLA LT3 LT 0.000000 55013.7800 0
+ 274 A7 1 CLA HB0 HB 0.000000 30478.0300 0
+ 275 A7 1 CLA PX1 PX 0.000000 46422.2000 0
+ 276 A7 1 CLA DT1 DT 0.000000 49195.2000 0
+ 277 A7 1 CLA AK1 AK 0.000000 34620.7800 0
+ 278 A7 1 CLA LT1 LT 0.000000 55013.7800 0
+ 279 A7 1 CLA PX2 PX 0.000000 46422.2000 0
+ 280 A7 1 CLA DT2 DT 0.000000 49195.2000 0
+ 281 A7 1 CLA AK2 AK 0.000000 34620.7800 0
+ 282 A7 1 CLA LT2 LT 0.000000 55013.7800 0
+ 283 A7 1 CLA PX3 PX 0.000000 46422.2000 0
+ 284 A7 1 CLA DT3 DT 0.000000 49195.2000 0
+ 285 A7 1 CLA AK3 AK 0.000000 34620.7800 0
+ 286 A7 1 CLA LT3 LT 0.000000 55013.7800 0
+ 287 B7 1 CLA HB0 HB 0.000000 30478.0300 0
+ 288 B7 1 CLA PX1 PX 0.000000 46422.2000 0
+ 289 B7 1 CLA DT1 DT 0.000000 49195.2000 0
+ 290 B7 1 CLA AK1 AK 0.000000 34620.7800 0
+ 291 B7 1 CLA LT1 LT 0.000000 55013.7800 0
+ 292 B7 1 CLA PX2 PX 0.000000 46422.2000 0
+ 293 B7 1 CLA DT2 DT 0.000000 49195.2000 0
+ 294 B7 1 CLA AK2 AK 0.000000 34620.7800 0
+ 295 B7 1 CLA LT2 LT 0.000000 55013.7800 0
+ 296 B7 1 CLA PX3 PX 0.000000 46422.2000 0
+ 297 B7 1 CLA DT3 DT 0.000000 49195.2000 0
+ 298 B7 1 CLA AK3 AK 0.000000 34620.7800 0
+ 299 B7 1 CLA LT3 LT 0.000000 55013.7800 0
+ 300 C7 1 CLA HB0 HB 0.000000 30478.0300 0
+ 301 C7 1 CLA PX1 PX 0.000000 46422.2000 0
+ 302 C7 1 CLA DT1 DT 0.000000 49195.2000 0
+ 303 C7 1 CLA AK1 AK 0.000000 34620.7800 0
+ 304 C7 1 CLA LT1 LT 0.000000 55013.7800 0
+ 305 C7 1 CLA PX2 PX 0.000000 46422.2000 0
+ 306 C7 1 CLA DT2 DT 0.000000 49195.2000 0
+ 307 C7 1 CLA AK2 AK 0.000000 34620.7800 0
+ 308 C7 1 CLA LT2 LT 0.000000 55013.7800 0
+ 309 C7 1 CLA PX3 PX 0.000000 46422.2000 0
+ 310 C7 1 CLA DT3 DT 0.000000 49195.2000 0
+ 311 C7 1 CLA AK3 AK 0.000000 34620.7800 0
+ 312 C7 1 CLA LT3 LT 0.000000 55013.7800 0
+ 313 A8 1 CLA HB0 HB 0.000000 30478.0300 0
+ 314 A8 1 CLA PX1 PX 0.000000 46422.2000 0
+ 315 A8 1 CLA DT1 DT 0.000000 49195.2000 0
+ 316 A8 1 CLA AK1 AK 0.000000 34620.7800 0
+ 317 A8 1 CLA LT1 LT 0.000000 55013.7800 0
+ 318 A8 1 CLA PX2 PX 0.000000 46422.2000 0
+ 319 A8 1 CLA DT2 DT 0.000000 49195.2000 0
+ 320 A8 1 CLA AK2 AK 0.000000 34620.7800 0
+ 321 A8 1 CLA LT2 LT 0.000000 55013.7800 0
+ 322 A8 1 CLA PX3 PX 0.000000 46422.2000 0
+ 323 A8 1 CLA DT3 DT 0.000000 49195.2000 0
+ 324 A8 1 CLA AK3 AK 0.000000 34620.7800 0
+ 325 A8 1 CLA LT3 LT 0.000000 55013.7800 0
+ 326 B8 1 CLA HB0 HB 0.000000 30478.0300 0
+ 327 B8 1 CLA PX1 PX 0.000000 46422.2000 0
+ 328 B8 1 CLA DT1 DT 0.000000 49195.2000 0
+ 329 B8 1 CLA AK1 AK 0.000000 34620.7800 0
+ 330 B8 1 CLA LT1 LT 0.000000 55013.7800 0
+ 331 B8 1 CLA PX2 PX 0.000000 46422.2000 0
+ 332 B8 1 CLA DT2 DT 0.000000 49195.2000 0
+ 333 B8 1 CLA AK2 AK 0.000000 34620.7800 0
+ 334 B8 1 CLA LT2 LT 0.000000 55013.7800 0
+ 335 B8 1 CLA PX3 PX 0.000000 46422.2000 0
+ 336 B8 1 CLA DT3 DT 0.000000 49195.2000 0
+ 337 B8 1 CLA AK3 AK 0.000000 34620.7800 0
+ 338 B8 1 CLA LT3 LT 0.000000 55013.7800 0
+ 339 C8 1 CLA HB0 HB 0.000000 30478.0300 0
+ 340 C8 1 CLA PX1 PX 0.000000 46422.2000 0
+ 341 C8 1 CLA DT1 DT 0.000000 49195.2000 0
+ 342 C8 1 CLA AK1 AK 0.000000 34620.7800 0
+ 343 C8 1 CLA LT1 LT 0.000000 55013.7800 0
+ 344 C8 1 CLA PX2 PX 0.000000 46422.2000 0
+ 345 C8 1 CLA DT2 DT 0.000000 49195.2000 0
+ 346 C8 1 CLA AK2 AK 0.000000 34620.7800 0
+ 347 C8 1 CLA LT2 LT 0.000000 55013.7800 0
+ 348 C8 1 CLA PX3 PX 0.000000 46422.2000 0
+ 349 C8 1 CLA DT3 DT 0.000000 49195.2000 0
+ 350 C8 1 CLA AK3 AK 0.000000 34620.7800 0
+ 351 C8 1 CLA LT3 LT 0.000000 55013.7800 0
+ 352 A9 1 CLA HB0 HB 0.000000 30478.0300 0
+ 353 A9 1 CLA PX1 PX 0.000000 46422.2000 0
+ 354 A9 1 CLA DT1 DT 0.000000 49195.2000 0
+ 355 A9 1 CLA AK1 AK 0.000000 34620.7800 0
+ 356 A9 1 CLA LT1 LT 0.000000 55013.7800 0
+ 357 A9 1 CLA PX2 PX 0.000000 46422.2000 0
+ 358 A9 1 CLA DT2 DT 0.000000 49195.2000 0
+ 359 A9 1 CLA AK2 AK 0.000000 34620.7800 0
+ 360 A9 1 CLA LT2 LT 0.000000 55013.7800 0
+ 361 A9 1 CLA PX3 PX 0.000000 46422.2000 0
+ 362 A9 1 CLA DT3 DT 0.000000 49195.2000 0
+ 363 A9 1 CLA AK3 AK 0.000000 34620.7800 0
+ 364 A9 1 CLA LT3 LT 0.000000 55013.7800 0
+ 365 B9 1 CLA HB0 HB 0.000000 30478.0300 0
+ 366 B9 1 CLA PX1 PX 0.000000 46422.2000 0
+ 367 B9 1 CLA DT1 DT 0.000000 49195.2000 0
+ 368 B9 1 CLA AK1 AK 0.000000 34620.7800 0
+ 369 B9 1 CLA LT1 LT 0.000000 55013.7800 0
+ 370 B9 1 CLA PX2 PX 0.000000 46422.2000 0
+ 371 B9 1 CLA DT2 DT 0.000000 49195.2000 0
+ 372 B9 1 CLA AK2 AK 0.000000 34620.7800 0
+ 373 B9 1 CLA LT2 LT 0.000000 55013.7800 0
+ 374 B9 1 CLA PX3 PX 0.000000 46422.2000 0
+ 375 B9 1 CLA DT3 DT 0.000000 49195.2000 0
+ 376 B9 1 CLA AK3 AK 0.000000 34620.7800 0
+ 377 B9 1 CLA LT3 LT 0.000000 55013.7800 0
+ 378 C9 1 CLA HB0 HB 0.000000 30478.0300 0
+ 379 C9 1 CLA PX1 PX 0.000000 46422.2000 0
+ 380 C9 1 CLA DT1 DT 0.000000 49195.2000 0
+ 381 C9 1 CLA AK1 AK 0.000000 34620.7800 0
+ 382 C9 1 CLA LT1 LT 0.000000 55013.7800 0
+ 383 C9 1 CLA PX2 PX 0.000000 46422.2000 0
+ 384 C9 1 CLA DT2 DT 0.000000 49195.2000 0
+ 385 C9 1 CLA AK2 AK 0.000000 34620.7800 0
+ 386 C9 1 CLA LT2 LT 0.000000 55013.7800 0
+ 387 C9 1 CLA PX3 PX 0.000000 46422.2000 0
+ 388 C9 1 CLA DT3 DT 0.000000 49195.2000 0
+ 389 C9 1 CLA AK3 AK 0.000000 34620.7800 0
+ 390 C9 1 CLA LT3 LT 0.000000 55013.7800 0
+ 391 A10 1 CLA HB0 HB 0.000000 30478.0300 0
+ 392 A10 1 CLA PX1 PX 0.000000 46422.2000 0
+ 393 A10 1 CLA DT1 DT 0.000000 49195.2000 0
+ 394 A10 1 CLA AK1 AK 0.000000 34620.7800 0
+ 395 A10 1 CLA LT1 LT 0.000000 55013.7800 0
+ 396 A10 1 CLA PX2 PX 0.000000 46422.2000 0
+ 397 A10 1 CLA DT2 DT 0.000000 49195.2000 0
+ 398 A10 1 CLA AK2 AK 0.000000 34620.7800 0
+ 399 A10 1 CLA LT2 LT 0.000000 55013.7800 0
+ 400 A10 1 CLA PX3 PX 0.000000 46422.2000 0
+ 401 A10 1 CLA DT3 DT 0.000000 49195.2000 0
+ 402 A10 1 CLA AK3 AK 0.000000 34620.7800 0
+ 403 A10 1 CLA LT3 LT 0.000000 55013.7800 0
+ 404 B10 1 CLA HB0 HB 0.000000 30478.0300 0
+ 405 B10 1 CLA PX1 PX 0.000000 46422.2000 0
+ 406 B10 1 CLA DT1 DT 0.000000 49195.2000 0
+ 407 B10 1 CLA AK1 AK 0.000000 34620.7800 0
+ 408 B10 1 CLA LT1 LT 0.000000 55013.7800 0
+ 409 B10 1 CLA PX2 PX 0.000000 46422.2000 0
+ 410 B10 1 CLA DT2 DT 0.000000 49195.2000 0
+ 411 B10 1 CLA AK2 AK 0.000000 34620.7800 0
+ 412 B10 1 CLA LT2 LT 0.000000 55013.7800 0
+ 413 B10 1 CLA PX3 PX 0.000000 46422.2000 0
+ 414 B10 1 CLA DT3 DT 0.000000 49195.2000 0
+ 415 B10 1 CLA AK3 AK 0.000000 34620.7800 0
+ 416 B10 1 CLA LT3 LT 0.000000 55013.7800 0
+ 417 C10 1 CLA HB0 HB 0.000000 30478.0300 0
+ 418 C10 1 CLA PX1 PX 0.000000 46422.2000 0
+ 419 C10 1 CLA DT1 DT 0.000000 49195.2000 0
+ 420 C10 1 CLA AK1 AK 0.000000 34620.7800 0
+ 421 C10 1 CLA LT1 LT 0.000000 55013.7800 0
+ 422 C10 1 CLA PX2 PX 0.000000 46422.2000 0
+ 423 C10 1 CLA DT2 DT 0.000000 49195.2000 0
+ 424 C10 1 CLA AK2 AK 0.000000 34620.7800 0
+ 425 C10 1 CLA LT2 LT 0.000000 55013.7800 0
+ 426 C10 1 CLA PX3 PX 0.000000 46422.2000 0
+ 427 C10 1 CLA DT3 DT 0.000000 49195.2000 0
+ 428 C10 1 CLA AK3 AK 0.000000 34620.7800 0
+ 429 C10 1 CLA LT3 LT 0.000000 55013.7800 0
+ 430 A11 1 CLA HB0 HB 0.000000 30478.0300 0
+ 431 A11 1 CLA PX1 PX 0.000000 46422.2000 0
+ 432 A11 1 CLA DT1 DT 0.000000 49195.2000 0
+ 433 A11 1 CLA AK1 AK 0.000000 34620.7800 0
+ 434 A11 1 CLA LT1 LT 0.000000 55013.7800 0
+ 435 A11 1 CLA PX2 PX 0.000000 46422.2000 0
+ 436 A11 1 CLA DT2 DT 0.000000 49195.2000 0
+ 437 A11 1 CLA AK2 AK 0.000000 34620.7800 0
+ 438 A11 1 CLA LT2 LT 0.000000 55013.7800 0
+ 439 A11 1 CLA PX3 PX 0.000000 46422.2000 0
+ 440 A11 1 CLA DT3 DT 0.000000 49195.2000 0
+ 441 A11 1 CLA AK3 AK 0.000000 34620.7800 0
+ 442 A11 1 CLA LT3 LT 0.000000 55013.7800 0
+ 443 B11 1 CLA HB0 HB 0.000000 30478.0300 0
+ 444 B11 1 CLA PX1 PX 0.000000 46422.2000 0
+ 445 B11 1 CLA DT1 DT 0.000000 49195.2000 0
+ 446 B11 1 CLA AK1 AK 0.000000 34620.7800 0
+ 447 B11 1 CLA LT1 LT 0.000000 55013.7800 0
+ 448 B11 1 CLA PX2 PX 0.000000 46422.2000 0
+ 449 B11 1 CLA DT2 DT 0.000000 49195.2000 0
+ 450 B11 1 CLA AK2 AK 0.000000 34620.7800 0
+ 451 B11 1 CLA LT2 LT 0.000000 55013.7800 0
+ 452 B11 1 CLA PX3 PX 0.000000 46422.2000 0
+ 453 B11 1 CLA DT3 DT 0.000000 49195.2000 0
+ 454 B11 1 CLA AK3 AK 0.000000 34620.7800 0
+ 455 B11 1 CLA LT3 LT 0.000000 55013.7800 0
+ 456 C11 1 CLA HB0 HB 0.000000 30478.0300 0
+ 457 C11 1 CLA PX1 PX 0.000000 46422.2000 0
+ 458 C11 1 CLA DT1 DT 0.000000 49195.2000 0
+ 459 C11 1 CLA AK1 AK 0.000000 34620.7800 0
+ 460 C11 1 CLA LT1 LT 0.000000 55013.7800 0
+ 461 C11 1 CLA PX2 PX 0.000000 46422.2000 0
+ 462 C11 1 CLA DT2 DT 0.000000 49195.2000 0
+ 463 C11 1 CLA AK2 AK 0.000000 34620.7800 0
+ 464 C11 1 CLA LT2 LT 0.000000 55013.7800 0
+ 465 C11 1 CLA PX3 PX 0.000000 46422.2000 0
+ 466 C11 1 CLA DT3 DT 0.000000 49195.2000 0
+ 467 C11 1 CLA AK3 AK 0.000000 34620.7800 0
+ 468 C11 1 CLA LT3 LT 0.000000 55013.7800 0
+
+ 432 !NBOND: bonds
+ 1 2 1 6 1 10 2 3
+ 3 4 4 5 6 7 7 8
+ 8 9 10 11 11 12 12 13
+ 14 15 14 19 14 23 15 16
+ 16 17 17 18 19 20 20 21
+ 21 22 23 24 24 25 25 26
+ 27 28 27 32 27 36 28 29
+ 29 30 30 31 32 33 33 34
+ 34 35 36 37 37 38 38 39
+ 40 41 40 45 40 49 41 42
+ 42 43 43 44 45 46 46 47
+ 47 48 49 50 50 51 51 52
+ 53 54 53 58 53 62 54 55
+ 55 56 56 57 58 59 59 60
+ 60 61 62 63 63 64 64 65
+ 66 67 66 71 66 75 67 68
+ 68 69 69 70 71 72 72 73
+ 73 74 75 76 76 77 77 78
+ 79 80 79 84 79 88 80 81
+ 81 82 82 83 84 85 85 86
+ 86 87 88 89 89 90 90 91
+ 92 93 92 97 92 101 93 94
+ 94 95 95 96 97 98 98 99
+ 99 100 101 102 102 103 103 104
+ 105 106 105 110 105 114 106 107
+ 107 108 108 109 110 111 111 112
+ 112 113 114 115 115 116 116 117
+ 118 119 118 123 118 127 119 120
+ 120 121 121 122 123 124 124 125
+ 125 126 127 128 128 129 129 130
+ 131 132 131 136 131 140 132 133
+ 133 134 134 135 136 137 137 138
+ 138 139 140 141 141 142 142 143
+ 144 145 144 149 144 153 145 146
+ 146 147 147 148 149 150 150 151
+ 151 152 153 154 154 155 155 156
+ 157 158 157 162 157 166 158 159
+ 159 160 160 161 162 163 163 164
+ 164 165 166 167 167 168 168 169
+ 170 171 170 175 170 179 171 172
+ 172 173 173 174 175 176 176 177
+ 177 178 179 180 180 181 181 182
+ 183 184 183 188 183 192 184 185
+ 185 186 186 187 188 189 189 190
+ 190 191 192 193 193 194 194 195
+ 196 197 196 201 196 205 197 198
+ 198 199 199 200 201 202 202 203
+ 203 204 205 206 206 207 207 208
+ 209 210 209 214 209 218 210 211
+ 211 212 212 213 214 215 215 216
+ 216 217 218 219 219 220 220 221
+ 222 223 222 227 222 231 223 224
+ 224 225 225 226 227 228 228 229
+ 229 230 231 232 232 233 233 234
+ 235 236 235 240 235 244 236 237
+ 237 238 238 239 240 241 241 242
+ 242 243 244 245 245 246 246 247
+ 248 249 248 253 248 257 249 250
+ 250 251 251 252 253 254 254 255
+ 255 256 257 258 258 259 259 260
+ 261 262 261 266 261 270 262 263
+ 263 264 264 265 266 267 267 268
+ 268 269 270 271 271 272 272 273
+ 274 275 274 279 274 283 275 276
+ 276 277 277 278 279 280 280 281
+ 281 282 283 284 284 285 285 286
+ 287 288 287 292 287 296 288 289
+ 289 290 290 291 292 293 293 294
+ 294 295 296 297 297 298 298 299
+ 300 301 300 305 300 309 301 302
+ 302 303 303 304 305 306 306 307
+ 307 308 309 310 310 311 311 312
+ 313 314 313 318 313 322 314 315
+ 315 316 316 317 318 319 319 320
+ 320 321 322 323 323 324 324 325
+ 326 327 326 331 326 335 327 328
+ 328 329 329 330 331 332 332 333
+ 333 334 335 336 336 337 337 338
+ 339 340 339 344 339 348 340 341
+ 341 342 342 343 344 345 345 346
+ 346 347 348 349 349 350 350 351
+ 352 353 352 357 352 361 353 354
+ 354 355 355 356 357 358 358 359
+ 359 360 361 362 362 363 363 364
+ 365 366 365 370 365 374 366 367
+ 367 368 368 369 370 371 371 372
+ 372 373 374 375 375 376 376 377
+ 378 379 378 383 378 387 379 380
+ 380 381 381 382 383 384 384 385
+ 385 386 387 388 388 389 389 390
+ 391 392 391 396 391 400 392 393
+ 393 394 394 395 396 397 397 398
+ 398 399 400 401 401 402 402 403
+ 404 405 404 409 404 413 405 406
+ 406 407 407 408 409 410 410 411
+ 411 412 413 414 414 415 415 416
+ 417 418 417 422 417 426 418 419
+ 419 420 420 421 422 423 423 424
+ 424 425 426 427 427 428 428 429
+ 430 431 430 435 430 439 431 432
+ 432 433 433 434 435 436 436 437
+ 437 438 439 440 440 441 441 442
+ 443 444 443 448 443 452 444 445
+ 445 446 446 447 448 449 449 450
+ 450 451 452 453 453 454 454 455
+ 456 457 456 461 456 465 457 458
+ 458 459 459 460 461 462 462 463
+ 463 464 465 466 466 467 467 468
+
+ 432 !NTHETA: angles
+ 1 10 11 1 6 7 1 2 3
+ 2 3 4 2 1 10 2 1 6
+ 3 4 5 6 7 8 6 1 10
+ 7 8 9 10 11 12 11 12 13
+ 14 23 24 14 19 20 14 15 16
+ 15 16 17 15 14 23 15 14 19
+ 16 17 18 19 20 21 19 14 23
+ 20 21 22 23 24 25 24 25 26
+ 27 36 37 27 32 33 27 28 29
+ 28 29 30 28 27 36 28 27 32
+ 29 30 31 32 33 34 32 27 36
+ 33 34 35 36 37 38 37 38 39
+ 40 49 50 40 45 46 40 41 42
+ 41 42 43 41 40 49 41 40 45
+ 42 43 44 45 46 47 45 40 49
+ 46 47 48 49 50 51 50 51 52
+ 53 62 63 53 58 59 53 54 55
+ 54 55 56 54 53 62 54 53 58
+ 55 56 57 58 59 60 58 53 62
+ 59 60 61 62 63 64 63 64 65
+ 66 75 76 66 71 72 66 67 68
+ 67 68 69 67 66 75 67 66 71
+ 68 69 70 71 72 73 71 66 75
+ 72 73 74 75 76 77 76 77 78
+ 79 88 89 79 84 85 79 80 81
+ 80 81 82 80 79 88 80 79 84
+ 81 82 83 84 85 86 84 79 88
+ 85 86 87 88 89 90 89 90 91
+ 92 101 102 92 97 98 92 93 94
+ 93 94 95 93 92 101 93 92 97
+ 94 95 96 97 98 99 97 92 101
+ 98 99 100 101 102 103 102 103 104
+ 105 114 115 105 110 111 105 106 107
+ 106 107 108 106 105 114 106 105 110
+ 107 108 109 110 111 112 110 105 114
+ 111 112 113 114 115 116 115 116 117
+ 118 127 128 118 123 124 118 119 120
+ 119 120 121 119 118 127 119 118 123
+ 120 121 122 123 124 125 123 118 127
+ 124 125 126 127 128 129 128 129 130
+ 131 140 141 131 136 137 131 132 133
+ 132 133 134 132 131 140 132 131 136
+ 133 134 135 136 137 138 136 131 140
+ 137 138 139 140 141 142 141 142 143
+ 144 153 154 144 149 150 144 145 146
+ 145 146 147 145 144 153 145 144 149
+ 146 147 148 149 150 151 149 144 153
+ 150 151 152 153 154 155 154 155 156
+ 157 166 167 157 162 163 157 158 159
+ 158 159 160 158 157 166 158 157 162
+ 159 160 161 162 163 164 162 157 166
+ 163 164 165 166 167 168 167 168 169
+ 170 179 180 170 175 176 170 171 172
+ 171 172 173 171 170 179 171 170 175
+ 172 173 174 175 176 177 175 170 179
+ 176 177 178 179 180 181 180 181 182
+ 183 192 193 183 188 189 183 184 185
+ 184 185 186 184 183 192 184 183 188
+ 185 186 187 188 189 190 188 183 192
+ 189 190 191 192 193 194 193 194 195
+ 196 205 206 196 201 202 196 197 198
+ 197 198 199 197 196 205 197 196 201
+ 198 199 200 201 202 203 201 196 205
+ 202 203 204 205 206 207 206 207 208
+ 209 218 219 209 214 215 209 210 211
+ 210 211 212 210 209 218 210 209 214
+ 211 212 213 214 215 216 214 209 218
+ 215 216 217 218 219 220 219 220 221
+ 222 231 232 222 227 228 222 223 224
+ 223 224 225 223 222 231 223 222 227
+ 224 225 226 227 228 229 227 222 231
+ 228 229 230 231 232 233 232 233 234
+ 235 244 245 235 240 241 235 236 237
+ 236 237 238 236 235 244 236 235 240
+ 237 238 239 240 241 242 240 235 244
+ 241 242 243 244 245 246 245 246 247
+ 248 257 258 248 253 254 248 249 250
+ 249 250 251 249 248 257 249 248 253
+ 250 251 252 253 254 255 253 248 257
+ 254 255 256 257 258 259 258 259 260
+ 261 270 271 261 266 267 261 262 263
+ 262 263 264 262 261 270 262 261 266
+ 263 264 265 266 267 268 266 261 270
+ 267 268 269 270 271 272 271 272 273
+ 274 283 284 274 279 280 274 275 276
+ 275 276 277 275 274 283 275 274 279
+ 276 277 278 279 280 281 279 274 283
+ 280 281 282 283 284 285 284 285 286
+ 287 296 297 287 292 293 287 288 289
+ 288 289 290 288 287 296 288 287 292
+ 289 290 291 292 293 294 292 287 296
+ 293 294 295 296 297 298 297 298 299
+ 300 309 310 300 305 306 300 301 302
+ 301 302 303 301 300 309 301 300 305
+ 302 303 304 305 306 307 305 300 309
+ 306 307 308 309 310 311 310 311 312
+ 313 322 323 313 318 319 313 314 315
+ 314 315 316 314 313 322 314 313 318
+ 315 316 317 318 319 320 318 313 322
+ 319 320 321 322 323 324 323 324 325
+ 326 335 336 326 331 332 326 327 328
+ 327 328 329 327 326 335 327 326 331
+ 328 329 330 331 332 333 331 326 335
+ 332 333 334 335 336 337 336 337 338
+ 339 348 349 339 344 345 339 340 341
+ 340 341 342 340 339 348 340 339 344
+ 341 342 343 344 345 346 344 339 348
+ 345 346 347 348 349 350 349 350 351
+ 352 361 362 352 357 358 352 353 354
+ 353 354 355 353 352 361 353 352 357
+ 354 355 356 357 358 359 357 352 361
+ 358 359 360 361 362 363 362 363 364
+ 365 374 375 365 370 371 365 366 367
+ 366 367 368 366 365 374 366 365 370
+ 367 368 369 370 371 372 370 365 374
+ 371 372 373 374 375 376 375 376 377
+ 378 387 388 378 383 384 378 379 380
+ 379 380 381 379 378 387 379 378 383
+ 380 381 382 383 384 385 383 378 387
+ 384 385 386 387 388 389 388 389 390
+ 391 400 401 391 396 397 391 392 393
+ 392 393 394 392 391 400 392 391 396
+ 393 394 395 396 397 398 396 391 400
+ 397 398 399 400 401 402 401 402 403
+ 404 413 414 404 409 410 404 405 406
+ 405 406 407 405 404 413 405 404 409
+ 406 407 408 409 410 411 409 404 413
+ 410 411 412 413 414 415 414 415 416
+ 417 426 427 417 422 423 417 418 419
+ 418 419 420 418 417 426 418 417 422
+ 419 420 421 422 423 424 422 417 426
+ 423 424 425 426 427 428 427 428 429
+ 430 439 440 430 435 436 430 431 432
+ 431 432 433 431 430 439 431 430 435
+ 432 433 434 435 436 437 435 430 439
+ 436 437 438 439 440 441 440 441 442
+ 443 452 453 443 448 449 443 444 445
+ 444 445 446 444 443 452 444 443 448
+ 445 446 447 448 449 450 448 443 452
+ 449 450 451 452 453 454 453 454 455
+ 456 465 466 456 461 462 456 457 458
+ 457 458 459 457 456 465 457 456 461
+ 458 459 460 461 462 463 461 456 465
+ 462 463 464 465 466 467 466 467 468
+
+ 0 !NPHI: dihedrals
+
+
+ 468 !NIMPHI: impropers
+ 1 2 3 4 1 6 7 8
+ 1 10 11 12 2 6 1 10
+ 2 1 6 7 2 1 10 11
+ 2 3 4 5 6 1 2 3
+ 6 1 10 11 6 7 8 9
+ 10 1 2 3 10 1 6 7
+ 10 11 12 13 14 15 16 17
+ 14 19 20 21 14 23 24 25
+ 15 19 14 23 15 14 19 20
+ 15 14 23 24 15 16 17 18
+ 19 14 15 16 19 14 23 24
+ 19 20 21 22 23 14 15 16
+ 23 14 19 20 23 24 25 26
+ 27 28 29 30 27 32 33 34
+ 27 36 37 38 28 32 27 36
+ 28 27 32 33 28 27 36 37
+ 28 29 30 31 32 27 28 29
+ 32 27 36 37 32 33 34 35
+ 36 27 28 29 36 27 32 33
+ 36 37 38 39 40 41 42 43
+ 40 45 46 47 40 49 50 51
+ 41 45 40 49 41 40 45 46
+ 41 40 49 50 41 42 43 44
+ 45 40 41 42 45 40 49 50
+ 45 46 47 48 49 40 41 42
+ 49 40 45 46 49 50 51 52
+ 53 54 55 56 53 58 59 60
+ 53 62 63 64 54 58 53 62
+ 54 53 58 59 54 53 62 63
+ 54 55 56 57 58 53 54 55
+ 58 53 62 63 58 59 60 61
+ 62 53 54 55 62 53 58 59
+ 62 63 64 65 66 67 68 69
+ 66 71 72 73 66 75 76 77
+ 67 71 66 75 67 66 71 72
+ 67 66 75 76 67 68 69 70
+ 71 66 67 68 71 66 75 76
+ 71 72 73 74 75 66 67 68
+ 75 66 71 72 75 76 77 78
+ 79 80 81 82 79 84 85 86
+ 79 88 89 90 80 84 79 88
+ 80 79 84 85 80 79 88 89
+ 80 81 82 83 84 79 80 81
+ 84 79 88 89 84 85 86 87
+ 88 79 80 81 88 79 84 85
+ 88 89 90 91 92 93 94 95
+ 92 97 98 99 92 101 102 103
+ 93 97 92 101 93 92 97 98
+ 93 92 101 102 93 94 95 96
+ 97 92 93 94 97 92 101 102
+ 97 98 99 100 101 92 93 94
+ 101 92 97 98 101 102 103 104
+ 105 106 107 108 105 110 111 112
+ 105 114 115 116 106 110 105 114
+ 106 105 110 111 106 105 114 115
+ 106 107 108 109 110 105 106 107
+ 110 105 114 115 110 111 112 113
+ 114 105 106 107 114 105 110 111
+ 114 115 116 117 118 119 120 121
+ 118 123 124 125 118 127 128 129
+ 119 123 118 127 119 118 123 124
+ 119 118 127 128 119 120 121 122
+ 123 118 119 120 123 118 127 128
+ 123 124 125 126 127 118 119 120
+ 127 118 123 124 127 128 129 130
+ 131 132 133 134 131 136 137 138
+ 131 140 141 142 132 136 131 140
+ 132 131 136 137 132 131 140 141
+ 132 133 134 135 136 131 132 133
+ 136 131 140 141 136 137 138 139
+ 140 131 132 133 140 131 136 137
+ 140 141 142 143 144 145 146 147
+ 144 149 150 151 144 153 154 155
+ 145 149 144 153 145 144 149 150
+ 145 144 153 154 145 146 147 148
+ 149 144 145 146 149 144 153 154
+ 149 150 151 152 153 144 145 146
+ 153 144 149 150 153 154 155 156
+ 157 158 159 160 157 162 163 164
+ 157 166 167 168 158 162 157 166
+ 158 157 162 163 158 157 166 167
+ 158 159 160 161 162 157 158 159
+ 162 157 166 167 162 163 164 165
+ 166 157 158 159 166 157 162 163
+ 166 167 168 169 170 171 172 173
+ 170 175 176 177 170 179 180 181
+ 171 175 170 179 171 170 175 176
+ 171 170 179 180 171 172 173 174
+ 175 170 171 172 175 170 179 180
+ 175 176 177 178 179 170 171 172
+ 179 170 175 176 179 180 181 182
+ 183 184 185 186 183 188 189 190
+ 183 192 193 194 184 188 183 192
+ 184 183 188 189 184 183 192 193
+ 184 185 186 187 188 183 184 185
+ 188 183 192 193 188 189 190 191
+ 192 183 184 185 192 183 188 189
+ 192 193 194 195 196 197 198 199
+ 196 201 202 203 196 205 206 207
+ 197 201 196 205 197 196 201 202
+ 197 196 205 206 197 198 199 200
+ 201 196 197 198 201 196 205 206
+ 201 202 203 204 205 196 197 198
+ 205 196 201 202 205 206 207 208
+ 209 210 211 212 209 214 215 216
+ 209 218 219 220 210 214 209 218
+ 210 209 214 215 210 209 218 219
+ 210 211 212 213 214 209 210 211
+ 214 209 218 219 214 215 216 217
+ 218 209 210 211 218 209 214 215
+ 218 219 220 221 222 223 224 225
+ 222 227 228 229 222 231 232 233
+ 223 227 222 231 223 222 227 228
+ 223 222 231 232 223 224 225 226
+ 227 222 223 224 227 222 231 232
+ 227 228 229 230 231 222 223 224
+ 231 222 227 228 231 232 233 234
+ 235 236 237 238 235 240 241 242
+ 235 244 245 246 236 240 235 244
+ 236 235 240 241 236 235 244 245
+ 236 237 238 239 240 235 236 237
+ 240 235 244 245 240 241 242 243
+ 244 235 236 237 244 235 240 241
+ 244 245 246 247 248 249 250 251
+ 248 253 254 255 248 257 258 259
+ 249 253 248 257 249 248 253 254
+ 249 248 257 258 249 250 251 252
+ 253 248 249 250 253 248 257 258
+ 253 254 255 256 257 248 249 250
+ 257 248 253 254 257 258 259 260
+ 261 262 263 264 261 266 267 268
+ 261 270 271 272 262 266 261 270
+ 262 261 266 267 262 261 270 271
+ 262 263 264 265 266 261 262 263
+ 266 261 270 271 266 267 268 269
+ 270 261 262 263 270 261 266 267
+ 270 271 272 273 274 275 276 277
+ 274 279 280 281 274 283 284 285
+ 275 279 274 283 275 274 279 280
+ 275 274 283 284 275 276 277 278
+ 279 274 275 276 279 274 283 284
+ 279 280 281 282 283 274 275 276
+ 283 274 279 280 283 284 285 286
+ 287 288 289 290 287 292 293 294
+ 287 296 297 298 288 292 287 296
+ 288 287 292 293 288 287 296 297
+ 288 289 290 291 292 287 288 289
+ 292 287 296 297 292 293 294 295
+ 296 287 288 289 296 287 292 293
+ 296 297 298 299 300 301 302 303
+ 300 305 306 307 300 309 310 311
+ 301 305 300 309 301 300 305 306
+ 301 300 309 310 301 302 303 304
+ 305 300 301 302 305 300 309 310
+ 305 306 307 308 309 300 301 302
+ 309 300 305 306 309 310 311 312
+ 313 314 315 316 313 318 319 320
+ 313 322 323 324 314 318 313 322
+ 314 313 318 319 314 313 322 323
+ 314 315 316 317 318 313 314 315
+ 318 313 322 323 318 319 320 321
+ 322 313 314 315 322 313 318 319
+ 322 323 324 325 326 327 328 329
+ 326 331 332 333 326 335 336 337
+ 327 331 326 335 327 326 331 332
+ 327 326 335 336 327 328 329 330
+ 331 326 327 328 331 326 335 336
+ 331 332 333 334 335 326 327 328
+ 335 326 331 332 335 336 337 338
+ 339 340 341 342 339 344 345 346
+ 339 348 349 350 340 344 339 348
+ 340 339 344 345 340 339 348 349
+ 340 341 342 343 344 339 340 341
+ 344 339 348 349 344 345 346 347
+ 348 339 340 341 348 339 344 345
+ 348 349 350 351 352 353 354 355
+ 352 357 358 359 352 361 362 363
+ 353 357 352 361 353 352 357 358
+ 353 352 361 362 353 354 355 356
+ 357 352 353 354 357 352 361 362
+ 357 358 359 360 361 352 353 354
+ 361 352 357 358 361 362 363 364
+ 365 366 367 368 365 370 371 372
+ 365 374 375 376 366 370 365 374
+ 366 365 370 371 366 365 374 375
+ 366 367 368 369 370 365 366 367
+ 370 365 374 375 370 371 372 373
+ 374 365 366 367 374 365 370 371
+ 374 375 376 377 378 379 380 381
+ 378 383 384 385 378 387 388 389
+ 379 383 378 387 379 378 383 384
+ 379 378 387 388 379 380 381 382
+ 383 378 379 380 383 378 387 388
+ 383 384 385 386 387 378 379 380
+ 387 378 383 384 387 388 389 390
+ 391 392 393 394 391 396 397 398
+ 391 400 401 402 392 396 391 400
+ 392 391 396 397 392 391 400 401
+ 392 393 394 395 396 391 392 393
+ 396 391 400 401 396 397 398 399
+ 400 391 392 393 400 391 396 397
+ 400 401 402 403 404 405 406 407
+ 404 409 410 411 404 413 414 415
+ 405 409 404 413 405 404 409 410
+ 405 404 413 414 405 406 407 408
+ 409 404 405 406 409 404 413 414
+ 409 410 411 412 413 404 405 406
+ 413 404 409 410 413 414 415 416
+ 417 418 419 420 417 422 423 424
+ 417 426 427 428 418 422 417 426
+ 418 417 422 423 418 417 426 427
+ 418 419 420 421 422 417 418 419
+ 422 417 426 427 422 423 424 425
+ 426 417 418 419 426 417 422 423
+ 426 427 428 429 430 431 432 433
+ 430 435 436 437 430 439 440 441
+ 431 435 430 439 431 430 435 436
+ 431 430 439 440 431 432 433 434
+ 435 430 431 432 435 430 439 440
+ 435 436 437 438 439 430 431 432
+ 439 430 435 436 439 440 441 442
+ 443 444 445 446 443 448 449 450
+ 443 452 453 454 444 448 443 452
+ 444 443 448 449 444 443 452 453
+ 444 445 446 447 448 443 444 445
+ 448 443 452 453 448 449 450 451
+ 452 443 444 445 452 443 448 449
+ 452 453 454 455 456 457 458 459
+ 456 461 462 463 456 465 466 467
+ 457 461 456 465 457 456 461 462
+ 457 456 465 466 457 458 459 460
+ 461 456 457 458 461 456 465 466
+ 461 462 463 464 465 456 457 458
+ 465 456 461 462 465 466 467 468
+
+ 0 !NDON: donors
+
+
+ 0 !NACC: acceptors
+
+
+ 0 !NNB
+
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0 0 0 0 0
+ 0 0 0 0
+
+ 1 0 !NGRP
+ 0 0 0
+
Property changes on: SwiftTutorials/UofC_2012-11-27-fusion/cg_clath_cage.psf
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftTutorials/UofC_2012-11-27-fusion/data/data.txt
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/data/data.txt (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/data/data.txt 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1 @@
+Hi Swift!
Added: SwiftTutorials/UofC_2012-11-27-fusion/par_cg_clath.inp
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/par_cg_clath.inp (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/par_cg_clath.inp 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,80 @@
+* Charmm Parameter file
+* For 13 bead CG clathrin model
+* Handmade by FXV - 7-21-11
+* Initial guess (very rough)
+
+BONDS
+!
+
+!V(bond) = Kb(b - b0)**2
+!
+!Kb: kcal/mole/A**2
+!b0: A
+!
+!atom type Kb b0
+!
+
+HB PX 0.5 85.5
+PX DT 0.018 135.2
+DT AK 0.045 124.2
+AK LT 0.08 94.1
+
+ANGLES
+!
+!V(angle) = Ktheta(Theta - Theta0)**2
+!
+!Ktheta: kcal/mole/rad**2
+!Theta0: degrees
+!
+!atom types Ktheta Theta0
+!
+PX HB PX 70.0 120.00
+DT PX HB 50.0 144.3
+AK DT PX 35.0 132.6
+LT AK DT 150.0 141.5
+
+DIHEDRALS
+!
+!V(dihedral) = Kchi(1 + cos(n(chi) - delta))
+!
+!Kchi: kcal/mole
+!n: multiplicity
+!delta: degrees
+!
+!atom types Kchi n delta
+!
+X X X X 0.0 1 0.0 ! No dihedrals
+
+IMPROPER
+!
+!V(improper) = Kpsi(psi - psi0)**2
+!
+!Kpsi: kcal/mole/rad**2
+!psi0: degrees
+!note that the second column of numbers (0) is ignored
+!
+!atom types Kpsi psi0
+!
+PX PX HB PX 200.00 0 161.17
+PX HB PX DT 10.0 0 -30.4
+HB PX DT AK 9.5 0 -16.1
+PX DT AK LT 45.0 0 26.1
+
+NONBONDED
+!
+!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]
+!
+!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)
+!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j
+!
+!atom ignored epsilon Rmin/2
+!
+HB 0.000000 HBEPS 43.075000
+PX 0.000000 PXEPS 18.425000
+DT 0.000000 DTEPS 10.455000
+AK 0.000000 AKEPS 25.975000
+LT 0.000000 LTEPS 36.905000
+
+
+END
+
Added: SwiftTutorials/UofC_2012-11-27-fusion/rmsd.temp.tcl
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/rmsd.temp.tcl (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/rmsd.temp.tcl 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,56 @@
+#====================================
+# THis script will measure the
+# the average angles, bond lengths
+# and dihedral angles.
+#
+# -FXV Oct, 2011
+#===================================
+
+mol delete all
+
+# set atom selection
+set seltext "type HB AK"
+
+# Set the initial frame
+set inifrm 200
+
+set psf cg_clath_cage.psf
+set pdb cg_clath_cage.pdb
+set dcd cg_clath_cage.dcd
+
+# Load input files
+mol load psf $psf
+# Load trajectory
+mol addfile $pdb type pdb
+mol addfile $dcd type dcd first $inifrm last -1 waitfor all
+
+# Get molecule information
+set mol [molinfo top]
+
+# Get the number of frames
+set nmfrm [molinfo $mol get numframes]
+puts "number of frames $nmfrm"
+
+# open rmsd file
+set frmsd [open rmsd.dat w]
+
+# Select atoms
+set ref [atomselect top $seltext frame 0]
+
+# Loop over the number of frames
+for {set ifrm 0} {$ifrm <= $nmfrm} {incr ifrm} {
+
+ set sel [atomselect top $seltext frame $ifrm]
+
+ set irmsd [measure rmsd $ref $sel]
+
+ lappend rmsdlist $irmsd
+
+
+}
+
+# Analysis
+puts $frmsd "B1 B2 [vecmean $rmsdlist]"
+
+exit
+
Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/catsn.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/catsn.swift (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/catsn.swift 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,12 @@
+type file;
+
+app (file o) cat (file i)
+{
+ cat @i stdout=@o;
+}
+
+file out[]<simple_mapper; location="outdir", prefix="f.",suffix=".out">;
+foreach j in [1:@toint(@arg("n","1"))] {
+ file data<"data.txt">;
+ out[j] = cat(data);
+}
Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script01.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script01.swift (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script01.swift 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,9 @@
+type file;
+
+app (file o) getinfo ()
+{
+ getinfo stdout=@o;
+}
+
+file info <"output/info.txt">;
+info = getinfo();
Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script02.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script02.swift (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script02.swift 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,13 @@
+type file;
+
+app (file o) getinfo ()
+{
+ getinfo stdout=@o;
+}
+
+foreach i in [0:24] {
+ string fname = @strcat("output/info.",i,".txt");
+ file info <single_file_mapper; file=fname>;
+ info = getinfo();
+}
+
Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script03.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script03.swift (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script03.swift 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,19 @@
+type file;
+
+app (file o) getinfo ()
+{
+ getinfo stdout=@o;
+}
+
+app (file o) filterinfo (file i)
+{
+ filterinfo @i @o;
+}
+
+foreach i in [0:24] {
+ string fname = @strcat("output/info.",i,".txt");
+ file info <single_file_mapper; file=fname>;
+ info = getinfo();
+ file filtered = filterinfo(info);
+}
+
Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script04.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script04.swift (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script04.swift 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,25 @@
+type file;
+
+app (file o) getinfo ()
+{
+ getinfo stdout=@o;
+}
+
+app (file o) filter (file i)
+{
+ filterinfo @i @o;
+}
+
+file filtered[];
+
+foreach i in [0:24] {
+ string fname = @strcat("output/info.",i,".txt");
+ file info <single_file_mapper; file=fname>;
+ info = getinfo();
+ // replace: filtered[i] = filter(info);
+ // with:
+ string filfname = ???
+ filfname =
+ filtered[i] =
+}
+
Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script05.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script05.swift (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script05.swift 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,30 @@
+type file;
+
+app (file o) getinfo ()
+{
+ getinfo stdout=@o;
+}
+
+app (file o) filter (file i)
+{
+ filterinfo @i @o;
+}
+
+app (file o) reduce (file i[])
+{
+ suminfo @filenames(i) stdout=@o;
+}
+
+file filtered[];
+
+foreach i in [0:24] {
+ string fname = @strcat("output/info.",i,".txt");
+ file info <single_file_mapper; file=fname>;
+ info = getinfo();
+ filtered[i] = filter(info);
+}
+
+file sum<"output/sum.data">;
+
+sum = reduce(filtered);
+
Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script06.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script06.swift (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script06.swift 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,9 @@
+type file;
+
+app (file r) testmpi ()
+{
+ testmpi;
+}
+
+file results <"output/results.tar">;
+results = testmpi();
Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.kml
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.kml (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.kml 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,451 @@
+<project><!-- CACHE ID fde29c67-b524-4558-b5f9-1228186b92ec-no-provenance -->
+ <import file="sys.xml"/>
+ <import file="scheduler.xml"/>
+ <import file="rlog.xml"/>
+ <import file="vdl.k"/>
+ <types>
+ <xs:schema targetNamespace="http://ci.uchicago.edu/swift/2009/02/swiftscript" xmlns="http://ci.uchicago.edu/swift/2009/02/swiftscript" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:xs="http://www.w3.org/2001/XMLSchema">
+ <xs:simpleType name="file">
+ <xs:restriction base="string"/>
+ </xs:simpleType>
+ </xs:schema>
+ </types>
+ <global name="swift#string#17013">
+ <vdl:new type="string" value=".dcd" />
+ </global>
+ <global name="swift#string#17006">
+ <vdl:new type="string" value="logs/rmsd-" />
+ </global>
+ <global name="swift#string#17012">
+ <vdl:new type="string" value="output/cg_clath_cage-" />
+ </global>
+ <global name="swift#string#17010">
+ <vdl:new type="string" value=".err.txt" />
+ </global>
+ <global name="swift#string#17001">
+ <vdl:new type="string" value="DT" />
+ </global>
+ <global name="swift#string#17017">
+ <vdl:new type="string" value=".dat" />
+ </global>
+ <global name="swift#string#17016">
+ <vdl:new type="string" value="_" />
+ </global>
+ <global name="swift#string#17000">
+ <vdl:new type="string" value="PX" />
+ </global>
+ <global name="swift#string#17015">
+ <vdl:new type="string" value="output/rmsd." />
+ </global>
+ <global name="swift#string#17008">
+ <vdl:new type="string" value=".out.txt" />
+ </global>
+ <global name="swift#string#17007">
+ <vdl:new type="string" value="-" />
+ </global>
+ <global name="swift#float#17003">
+ <vdl:new type="float" value="1.0" />
+ </global>
+ <global name="swift#float#17002">
+ <vdl:new type="float" value="0.0" />
+ </global>
+ <global name="swift#float#17004">
+ <vdl:new type="float" value="0.5" />
+ </global>
+ <element name="rmsd" arguments="o,e,dcdf,datf,b1_val,b2_val,b1_name,b2_name,namd_input_file,namd_params_file,vmd_script_file,psf_file,pdb_file" _defline="3">
+
+
+
+
+
+
+
+
+
+
+
+
+
+ <unitStart name="rmsd" line="3" type="PROCEDURE" outputs="o,e,dcdf,datf"/>
+ <vdl:execute>
+ <vdl:tr>rmsd</vdl:tr>
+ <vdl:stagein var="{b1_val}"/>
+ <vdl:stagein var="{b2_val}"/>
+ <vdl:stagein var="{b1_name}"/>
+ <vdl:stagein var="{b2_name}"/>
+ <vdl:stagein var="{namd_input_file}"/>
+ <vdl:stagein var="{namd_params_file}"/>
+ <vdl:stagein var="{vmd_script_file}"/>
+ <vdl:stagein var="{psf_file}"/>
+ <vdl:stagein var="{pdb_file}"/>
+ <vdl:stageout var="{o}"/>
+ <vdl:stageout var="{e}"/>
+ <vdl:stageout var="{dcdf}"/>
+ <vdl:stageout var="{datf}"/>
+
+ <vdl:arguments>
+ <variable>b1_val</variable>
+ <variable>b2_val</variable>
+ <variable>b1_name</variable>
+ <variable>b2_name</variable>
+ <swiftscript:filename _traceline="5">
+ <variable>namd_input_file</variable>
+ </swiftscript:filename>
+ <swiftscript:filename _traceline="5">
+ <variable>namd_params_file</variable>
+ </swiftscript:filename>
+ <swiftscript:filename _traceline="5">
+ <variable>vmd_script_file</variable>
+ </swiftscript:filename>
+ </vdl:arguments>
+ <vdl:stdout>
+ <swiftscript:filename _traceline="5">
+ <variable>o</variable>
+ </swiftscript:filename>
+ </vdl:stdout><vdl:stderr>
+ <swiftscript:filename _traceline="5">
+ <variable>e</variable>
+ </swiftscript:filename>
+ </vdl:stderr>
+ </vdl:execute>
+ <vdl:closedataset var="{o}"/>
+ <vdl:closedataset var="{e}"/>
+ <vdl:closedataset var="{dcdf}"/>
+ <vdl:closedataset var="{datf}"/>
+ <unitEnd name="rmsd" line="3" type="PROCEDURE"/></element>
+
+ <set name="b1name">
+ <vdl:new type="string" dbgname="b1name" waitfor="88000" _defline="9"/>
+ </set>
+
+ <set name="b2name">
+ <vdl:new type="string" dbgname="b2name" waitfor="88001" _defline="10"/>
+ </set>
+
+ <set name="b1min">
+ <vdl:new type="float" dbgname="b1min" waitfor="88002" _defline="13"/>
+ </set>
+
+ <set name="b1max">
+ <vdl:new type="float" dbgname="b1max" waitfor="88003" _defline="14"/>
+ </set>
+
+ <set name="b2min">
+ <vdl:new type="float" dbgname="b2min" waitfor="88004" _defline="15"/>
+ </set>
+
+ <set name="b2max">
+ <vdl:new type="float" dbgname="b2max" waitfor="88005" _defline="16"/>
+ </set>
+
+ <set name="delta">
+ <vdl:new type="float" dbgname="delta" waitfor="88006" _defline="19"/>
+ </set>
+
+ <set name="namd_params">
+ <vdl:new type="file" dbgname="namd_params" _defline="22">
+ <vdl:mapping descriptor="single_file_mapper">
+ <vdl:parameter name="file" value="par_cg_clath.inp"/>
+ <vdl:parameter name="swift#input" value="true" />
+ </vdl:mapping>
+ </vdl:new>
+ </set>
+
+ <set name="namd_input">
+ <vdl:new type="file" dbgname="namd_input" _defline="23">
+ <vdl:mapping descriptor="single_file_mapper">
+ <vdl:parameter name="file" value="cg_clath_cage.conf"/>
+ <vdl:parameter name="swift#input" value="true" />
+ </vdl:mapping>
+ </vdl:new>
+ </set>
+
+ <set name="vmd_script">
+ <vdl:new type="file" dbgname="vmd_script" _defline="24">
+ <vdl:mapping descriptor="single_file_mapper">
+ <vdl:parameter name="file" value="rmsd.temp.tcl"/>
+ <vdl:parameter name="swift#input" value="true" />
+ </vdl:mapping>
+ </vdl:new>
+ </set>
+
+ <set name="psf">
+ <vdl:new type="file" dbgname="psf" _defline="25">
+ <vdl:mapping descriptor="single_file_mapper">
+ <vdl:parameter name="file" value="cg_clath_cage.psf"/>
+ <vdl:parameter name="swift#input" value="true" />
+ </vdl:mapping>
+ </vdl:new>
+ </set>
+
+ <set name="pdb">
+ <vdl:new type="file" dbgname="pdb" _defline="26">
+ <vdl:mapping descriptor="single_file_mapper">
+ <vdl:parameter name="file" value="cg_clath_cage.pdb"/>
+ <vdl:parameter name="swift#input" value="true" />
+ </vdl:mapping>
+ </vdl:new>
+ </set>
+
+ <set name="dats">
+ <vdl:new type="file[float][float]" dbgname="dats" waitfor="88013" _defline="27">
+ <vdl:mapping descriptor="concurrent_mapper">
+ <vdl:parameter name="prefix">dats-345532ce-25ec-45f9-933b-4d188d42079b</vdl:parameter>
+ </vdl:mapping>
+ </vdl:new>
+ </set>
+
+ <restartLog>
+ <vdl:mains>
+ <vdl:startprogressticker />
+ <vdl:mainp>
+ <uparallel>
+ <sequential>
+ <unitStart type="SCOPE" outputs="b1name"/>
+ <vdl:setfieldvalue _traceline="10">
+ <variable>b1name</variable>
+ <variable>swift#string#17000</variable>
+ </vdl:setfieldvalue>
+ <partialCloseDataset var="{b1name}" closeID="88000" />
+ <unitEnd type="SCOPE"/>
+ </sequential>
+ <sequential>
+ <unitStart type="SCOPE" outputs="b2name"/>
+ <vdl:setfieldvalue _traceline="13">
+ <variable>b2name</variable>
+ <variable>swift#string#17001</variable>
+ </vdl:setfieldvalue>
+ <partialCloseDataset var="{b2name}" closeID="88001" />
+ <unitEnd type="SCOPE"/>
+ </sequential>
+ <sequential>
+ <unitStart type="SCOPE" outputs="b1min"/>
+ <vdl:setfieldvalue _traceline="14">
+ <variable>b1min</variable>
+ <variable>swift#float#17002</variable>
+ </vdl:setfieldvalue>
+ <partialCloseDataset var="{b1min}" closeID="88002" />
+ <unitEnd type="SCOPE"/>
+ </sequential>
+ <sequential>
+ <unitStart type="SCOPE" outputs="b1max"/>
+ <vdl:setfieldvalue _traceline="15">
+ <variable>b1max</variable>
+ <variable>swift#float#17003</variable>
+ </vdl:setfieldvalue>
+ <partialCloseDataset var="{b1max}" closeID="88003" />
+ <unitEnd type="SCOPE"/>
+ </sequential>
+ <sequential>
+ <unitStart type="SCOPE" outputs="b2min"/>
+ <vdl:setfieldvalue _traceline="16">
+ <variable>b2min</variable>
+ <variable>swift#float#17002</variable>
+ </vdl:setfieldvalue>
+ <partialCloseDataset var="{b2min}" closeID="88004" />
+ <unitEnd type="SCOPE"/>
+ </sequential>
+ <sequential>
+ <unitStart type="SCOPE" outputs="b2max"/>
+ <vdl:setfieldvalue _traceline="19">
+ <variable>b2max</variable>
+ <variable>swift#float#17003</variable>
+ </vdl:setfieldvalue>
+ <partialCloseDataset var="{b2max}" closeID="88005" />
+ <unitEnd type="SCOPE"/>
+ </sequential>
+ <sequential>
+ <unitStart type="SCOPE" outputs="delta"/>
+ <vdl:setfieldvalue _traceline="22">
+ <variable>delta</variable>
+ <variable>swift#float#17004</variable>
+ </vdl:setfieldvalue>
+ <partialCloseDataset var="{delta}" closeID="88006" />
+ <unitEnd type="SCOPE"/>
+ </sequential>
+ <sequential>
+ <unitStart type="SCOPE" outputs="dats"/>
+ <vdl:tparallelFor name="$" _traceline="29"
+ _vvar="b1">
+ <getarrayiterator><sequential>
+ <set name="swift#from"><variable>b1min</variable></set>
+ <set name="swift#to"><variable>b1max</variable></set>
+ <set name="swift#step"><variable>delta</variable></set>
+ <set name="swift#rangeout">
+ <vdl:range>
+ <argument name="from"><variable>swift#from</variable></argument>
+ <argument name="to"><variable>swift#to</variable></argument>
+ <argument name="step"><variable>swift#step</variable></argument>
+ </vdl:range>
+ </set>
+
+ <variable>swift#rangeout</variable>
+ </sequential></getarrayiterator>
+ <set names="$$, b1">
+ <each items="{$}"/>
+ </set>
+ <unitStart line="29" type="FOREACH_IT"/>
+
+ <sequentialWithID>
+ <sequential>
+ <vdl:tparallelFor name="$"
+ _vvar="b2">
+ <getarrayiterator><sequential>
+ <set name="swift#from"><variable>b2min</variable></set>
+ <set name="swift#to"><variable>b2max</variable></set>
+ <set name="swift#step"><variable>delta</variable></set>
+ <set name="swift#rangeout">
+ <vdl:range>
+ <argument name="from"><variable>swift#from</variable></argument>
+ <argument name="to"><variable>swift#to</variable></argument>
+ <argument name="step"><variable>swift#step</variable></argument>
+ </vdl:range>
+ </set>
+
+ <variable>swift#rangeout</variable>
+ </sequential></getarrayiterator>
+ <set names="$$, b2">
+ <each items="{$}"/>
+ </set>
+ <unitStart line="30" type="FOREACH_IT"/>
+
+ <set name="swift#mapper#17005">
+ <vdl:new type="string" dbgname="swift#mapper#17005" waitfor="" _defline=""/>
+ </set>
+
+ <set name="output">
+ <vdl:new type="file" dbgname="output" waitfor="88008" _defline="31">
+ <vdl:mapping descriptor="single_file_mapper">
+ <vdl:parameter name="file"><variable>swift#mapper#17005</variable></vdl:parameter>
+ </vdl:mapping>
+ </vdl:new>
+ </set>
+
+ <set name="swift#mapper#17009">
+ <vdl:new type="string" dbgname="swift#mapper#17009" waitfor="" _defline=""/>
+ </set>
+
+ <set name="error">
+ <vdl:new type="file" dbgname="error" waitfor="88009" _defline="32">
+ <vdl:mapping descriptor="single_file_mapper">
+ <vdl:parameter name="file"><variable>swift#mapper#17009</variable></vdl:parameter>
+ </vdl:mapping>
+ </vdl:new>
+ </set>
+
+ <set name="swift#mapper#17011">
+ <vdl:new type="string" dbgname="swift#mapper#17011" waitfor="" _defline=""/>
+ </set>
+
+ <set name="dcd">
+ <vdl:new type="file" dbgname="dcd" waitfor="88010" _defline="33">
+ <vdl:mapping descriptor="single_file_mapper">
+ <vdl:parameter name="file"><variable>swift#mapper#17011</variable></vdl:parameter>
+ </vdl:mapping>
+ </vdl:new>
+ </set>
+
+ <set name="swift#mapper#17014">
+ <vdl:new type="string" dbgname="swift#mapper#17014" waitfor="" _defline=""/>
+ </set>
+
+ <set name="dat">
+ <vdl:new type="file" dbgname="dat" waitfor="88011" _defline="34">
+ <vdl:mapping descriptor="single_file_mapper">
+ <vdl:parameter name="file"><variable>swift#mapper#17014</variable></vdl:parameter>
+ </vdl:mapping>
+ </vdl:new>
+ </set>
+
+ <uparallel>
+ <sequential>
+ <vdl:setfieldvalue _traceline="-1">
+ <variable>swift#mapper#17005</variable>
+ <swiftscript:strcat _traceline="31">
+ <variable>swift#string#17006</variable><variable>b1</variable><variable>swift#string#17007</variable><variable>b2</variable><variable>swift#string#17008</variable>
+ </swiftscript:strcat>
+ </vdl:setfieldvalue>
+ </sequential>
+ <sequential>
+ <vdl:setfieldvalue _traceline="-1">
+ <variable>swift#mapper#17009</variable>
+ <swiftscript:strcat _traceline="32">
+ <variable>swift#string#17006</variable><variable>b1</variable><variable>swift#string#17007</variable><variable>b2</variable><variable>swift#string#17010</variable>
+ </swiftscript:strcat>
+ </vdl:setfieldvalue>
+ </sequential>
+ <sequential>
+ <vdl:setfieldvalue _traceline="-1">
+ <variable>swift#mapper#17011</variable>
+ <swiftscript:strcat _traceline="33">
+ <variable>swift#string#17012</variable><variable>b1</variable><variable>swift#string#17007</variable><variable>b2</variable><variable>swift#string#17013</variable>
+ </swiftscript:strcat>
+ </vdl:setfieldvalue>
+ </sequential>
+ <sequential>
+ <vdl:setfieldvalue _traceline="-1">
+ <variable>swift#mapper#17014</variable>
+ <swiftscript:strcat _traceline="34">
+ <variable>swift#string#17015</variable><variable>b1name</variable><variable>b1</variable><variable>swift#string#17016</variable><variable>b2name</variable><variable>b2</variable><variable>swift#string#17017</variable>
+ </swiftscript:strcat>
+ </vdl:setfieldvalue>
+ </sequential>
+ <sequential>
+ <vdl:setfieldvalue _traceline="36">
+ <vdl:getfieldsubscript>
+ <argument name="var"><vdl:getfieldsubscript>
+ <argument name="var"><variable>dats</variable></argument>
+ <argument name="subscript"><variable>b1</variable></argument>
+ </vdl:getfieldsubscript></argument>
+ <argument name="subscript"><variable>b2</variable></argument>
+ </vdl:getfieldsubscript>
+ <variable>dat</variable>
+ </vdl:setfieldvalue>
+ </sequential>
+ <sequential>
+ <unitStart type="SCOPE" outputs="output,error,dcd,dat"/>
+ <rmsd _traceline="36">
+ <variable>output</variable>
+ <variable>error</variable>
+ <variable>dcd</variable>
+ <variable>dat</variable>
+ <variable>b1</variable>
+ <variable>b2</variable>
+ <variable>b1name</variable>
+ <variable>b2name</variable>
+ <variable>namd_input</variable>
+ <variable>namd_params</variable>
+ <variable>vmd_script</variable>
+ <variable>psf</variable>
+ <variable>pdb</variable>
+ </rmsd>
+ <unitEnd type="SCOPE"/>
+ </sequential>
+ </uparallel>
+ <vdl:cleandataset var="{dat}"/>
+ <vdl:cleandataset var="{error}"/>
+ <vdl:cleandataset var="{dcd}"/>
+ <vdl:cleandataset var="{output}"/>
+ <unitEnd line="30" type="FOREACH_IT"/>
+ </vdl:tparallelFor>
+ </sequential>
+ </sequentialWithID>
+
+ <unitEnd line="29" type="FOREACH_IT"/>
+ </vdl:tparallelFor>
+ <partialCloseDataset var="{dats}" closeID="88013" />
+ <unitEnd type="SCOPE"/>
+ </sequential>
+ </uparallel>
+ </vdl:mainp>
+ <vdl:stopprogressticker />
+ </vdl:mains>
+ </restartLog>
+ <vdl:cleandataset var="{namd_params}"/>
+ <vdl:cleandataset var="{vmd_script}"/>
+ <vdl:cleandataset var="{psf}"/>
+ <vdl:cleandataset var="{namd_input}"/>
+ <vdl:cleandataset var="{pdb}"/>
+ <vdl:cleandataset var="{dats}"/>
+ <vdl:cleandataset shutdown="true"/>
+</project>
Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swift
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swift (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swift 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,38 @@
+type file;
+
+app (file o, file e, file dcdf, file datf) rmsd (float b1_val, float b2_val, string b1_name, string b2_name, file namd_input_file, file namd_params_file, file vmd_script_file, file psf_file, file pdb_file)
+{
+ rmsd b1_val b2_val b1_name b2_name @namd_input_file @namd_params_file @vmd_script_file stdout=@o stderr=@e;
+}
+
+# Bead names
+string b1name = "PX";
+string b2name = "DT";
+
+# Bead ranges
+float b1min=0.0;
+float b1max=1.0;
+float b2min=0.0;
+float b2max=1.0;
+
+# Delta
+float delta=0.5;
+
+# Files
+file namd_params <"par_cg_clath.inp">;
+file namd_input <"cg_clath_cage.conf">;
+file vmd_script <"rmsd.temp.tcl">;
+file psf <"cg_clath_cage.psf">;
+file pdb <"cg_clath_cage.pdb">;
+file[float][float] dats;
+
+foreach b1 in [b1min:b1max:delta] {
+ foreach b2 in [b2min:b2max:delta] {
+ file output <single_file_mapper; file=@strcat("logs/rmsd-", b1, "-", b2, ".out.txt")>;
+ file error <single_file_mapper; file=@strcat("logs/rmsd-", b1, "-", b2, ".err.txt")>;
+ file dcd <single_file_mapper; file=@strcat("output/cg_clath_cage-", b1, "-", b2, ".dcd")>;
+ file dat <single_file_mapper; file=@strcat("output/rmsd.", b1name, b1, "_", b2name, b2, ".dat")>;
+ dats[b1][b2] = dat;
+ (output, error, dcd, dat) = rmsd(b1, b2, b1name, b2name, namd_input, namd_params, vmd_script, psf, pdb);
+ }
+}
Added: SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swiftx
===================================================================
--- SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swiftx (rev 0)
+++ SwiftTutorials/UofC_2012-11-27-fusion/scripts/script07.swiftx 2012-12-05 20:21:35 UTC (rev 6099)
@@ -0,0 +1,157 @@
+<program xmlns="http://ci.uchicago.edu/swift/2009/02/swiftscript"
+ xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+ xmlns:xs="http://www.w3.org/2001/XMLSchema">
+ <types>
+ <type>
+ <typename>file</typename>
+ <typealias>string</typealias>
+ <typestructure></typestructure>
+ </type>
+ </types>
+ <procedure name="rmsd" src="line 3">
+
+ <output name="o" type="file" xsi:nil="true"/>
+
+ <output name="e" type="file" xsi:nil="true"/>
+
+ <output name="dcdf" type="file" xsi:nil="true"/>
+
+ <output name="datf" type="file" xsi:nil="true"/>
+
+ <input name="b1_val" type="float" xsi:nil="true"/>
+
+ <input name="b2_val" type="float" xsi:nil="true"/>
+
+ <input name="b1_name" type="string" xsi:nil="true"/>
+
+ <input name="b2_name" type="string" xsi:nil="true"/>
+
+ <input name="namd_input_file" type="file" xsi:nil="true"/>
+
+ <input name="namd_params_file" type="file" xsi:nil="true"/>
+
+ <input name="vmd_script_file" type="file" xsi:nil="true"/>
+
+ <input name="psf_file" type="file" xsi:nil="true"/>
+
+ <input name="pdb_file" type="file" xsi:nil="true"/>
+ <binding>
+ <application src="line 3">
+ <executable>rmsd</executable>
+ <stdout><function name="filename" src="line 5">
+ <variableReference>o</variableReference></function></stdout><stderr><function name="filename" src="line 5">
+ <variableReference>e</variableReference></function></stderr><variableReference>b1_val</variableReference><variableReference>b2_val</variableReference><variableReference>b1_name</variableReference><variableReference>b2_name</variableReference><function name="filename" src="line 5">
+ <variableReference>namd_input_file</variableReference></function><function name="filename" src="line 5">
+ <variableReference>namd_params_file</variableReference></function><function name="filename" src="line 5">
+ <variableReference>vmd_script_file</variableReference></function> </application>
+ </binding>
+ </procedure>
+ <variable name="b1name" type="string" isGlobal="false" xsi:nil="true" src="line 9"/>
+ <assign src="line 10">
+ <variableReference>b1name</variableReference>
+ <stringConstant>PX</stringConstant>
+ </assign>
+ <variable name="b2name" type="string" isGlobal="false" xsi:nil="true" src="line 10"/>
+ <assign src="line 13">
+ <variableReference>b2name</variableReference>
+ <stringConstant>DT</stringConstant>
+ </assign>
+ <variable name="b1min" type="float" isGlobal="false" xsi:nil="true" src="line 13"/>
+ <assign src="line 14">
+ <variableReference>b1min</variableReference>
+ <floatConstant>0.0</floatConstant>
+ </assign>
+ <variable name="b1max" type="float" isGlobal="false" xsi:nil="true" src="line 14"/>
+ <assign src="line 15">
+ <variableReference>b1max</variableReference>
+ <floatConstant>1.0</floatConstant>
+ </assign>
+ <variable name="b2min" type="float" isGlobal="false" xsi:nil="true" src="line 15"/>
+ <assign src="line 16">
+ <variableReference>b2min</variableReference>
+ <floatConstant>0.0</floatConstant>
+ </assign>
+ <variable name="b2max" type="float" isGlobal="false" xsi:nil="true" src="line 16"/>
+ <assign src="line 19">
+ <variableReference>b2max</variableReference>
+ <floatConstant>1.0</floatConstant>
+ </assign>
+ <variable name="delta" type="float" isGlobal="false" xsi:nil="true" src="line 19"/>
+ <assign src="line 22">
+ <variableReference>delta</variableReference>
+ <floatConstant>0.5</floatConstant>
+ </assign>
+ <variable name="namd_params" type="file" isGlobal="false" src="line 22"><file name="par_cg_clath.inp"/></variable>
+ <variable name="namd_input" type="file" isGlobal="false" src="line 23"><file name="cg_clath_cage.conf"/></variable>
+ <variable name="vmd_script" type="file" isGlobal="false" src="line 24"><file name="rmsd.temp.tcl"/></variable>
+ <variable name="psf" type="file" isGlobal="false" src="line 25"><file name="cg_clath_cage.psf"/></variable>
+ <variable name="pdb" type="file" isGlobal="false" src="line 26"><file name="cg_clath_cage.pdb"/></variable>
+ <variable name="dats" type="file[float][float]" isGlobal="false" xsi:nil="true" src="line 27"/>
+ <foreach var="b1" src="line 29">
+ <in>
+ <range>
+ <variableReference>b1min</variableReference>
+ <variableReference>b1max</variableReference>
+ <variableReference>delta</variableReference>
+ </range>
+ </in>
+ <body><foreach var="b2" src="line 30">
+ <in>
+ <range>
+ <variableReference>b2min</variableReference>
+ <variableReference>b2max</variableReference>
+ <variableReference>delta</variableReference>
+ </range>
+ </in>
+ <body><variable name="output" type="file" isGlobal="false" src="line 31">
+ <mapping descriptor="single_file_mapper">
+ <param name="file"><function name="strcat" src="line 31">
+ <stringConstant>logs/rmsd-</stringConstant><variableReference>b1</variableReference><stringConstant>-</stringConstant><variableReference>b2</variableReference><stringConstant>.out.txt</stringConstant></function></param>
+ </mapping>
+ </variable>
+ <variable name="error" type="file" isGlobal="false" src="line 32">
+ <mapping descriptor="single_file_mapper">
+ <param name="file"><function name="strcat" src="line 32">
+ <stringConstant>logs/rmsd-</stringConstant><variableReference>b1</variableReference><stringConstant>-</stringConstant><variableReference>b2</variableReference><stringConstant>.err.txt</stringConstant></function></param>
+ </mapping>
+ </variable>
+ <variable name="dcd" type="file" isGlobal="false" src="line 33">
+ <mapping descriptor="single_file_mapper">
+ <param name="file"><function name="strcat" src="line 33">
+ <stringConstant>output/cg_clath_cage-</stringConstant><variableReference>b1</variableReference><stringConstant>-</stringConstant><variableReference>b2</variableReference><stringConstant>.dcd</stringConstant></function></param>
+ </mapping>
+ </variable>
+ <variable name="dat" type="file" isGlobal="false" src="line 34">
+ <mapping descriptor="single_file_mapper">
+ <param name="file"><function name="strcat" src="line 34">
+ <stringConstant>output/rmsd.</stringConstant><variableReference>b1name</variableReference><variableReference>b1</variableReference><stringConstant>_</stringConstant><variableReference>b2name</variableReference><variableReference>b2</variableReference><stringConstant>.dat</stringConstant></function></param>
+ </mapping>
+ </variable>
+ <assign src="line 36">
+ <arraySubscript>
+ <arraySubscript>
+ <variableReference>dats</variableReference>
+ <variableReference>b1</variableReference>
+ </arraySubscript>
+ <variableReference>b2</variableReference>
+ </arraySubscript>
+ <variableReference>dat</variableReference>
+ </assign>
+ <call proc="rmsd" src="line 36">
+ <output><variableReference>output</variableReference></output>
+ <output><variableReference>error</variableReference></output>
+ <output><variableReference>dcd</variableReference></output>
+ <output><variableReference>dat</variableReference></output>
+ <input><variableReference>b1</variableReference></input>
+ <input><variableReference>b2</variableReference></input>
+ <input><variableReference>b1name</variableReference></input>
+ <input><variableReference>b2name</variableReference></input>
+ <input><variableReference>namd_input</variableReference></input>
+ <input><variableReference>namd_params</variableReference></input>
+ <input><variableReference>vmd_script</variableReference></input>
+ <input><variableReference>psf</variableReference></input>
+ <input><variableReference>pdb</variableReference></input>
+ </call></body>
+ </foreach></body>
+ </foreach>
+</program>
More information about the Swift-commit
mailing list