MSL Programs::repackSideChains - Revision history

Jedonald at 19:21, 10 July 2012

2012-07-10T19:21:50Z

Sab at 05:34, 22 November 2011

2011-11-22T05:34:20Z

Sab: /* Options */

2011-11-21T23:21:54Z

‎Options

Sab: /* Examples */

2011-11-21T22:56:40Z

‎Examples

Sab: /* Examples */

2011-11-21T22:56:21Z

‎Examples

Sab: /* Options */

2011-11-21T22:55:38Z

‎Options

Dwkulp at 22:57, 18 November 2011

2011-11-18T22:57:31Z

Dwkulp: Created page with " ==repackSideChains== A program to repack side chains of an input structure. ==Options== --pdb FILE.pdb PDB structure to analyze == Details == repacking will ......"

2011-11-18T16:22:07Z

Created page with " ==repackSideChains== A program to repack side chains of an input structure. ==Options== --pdb FILE.pdb PDB structure to analyze == Details == repacking will ......"

New page

==repackSideChains==

A program to repack side chains of an input structure.

==Options==
--pdb FILE.pdb PDB structure to analyze

== Details ==
repacking will ...

==Examples==

> '''repackSideChains --pdb ~/Downloads/1MEL.pdb'''
SOME OUTPUT HERE FOR 1MEL.pdb
....

==Source from SourceForge==

[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/repackSideChains.h?&view=markup repackSideChains.h]

[http://mslib.svn.sourceforge.net/viewvc/mslib/trunk/programs/repackSideChains.cpp?&view=markup repackSideChains.cpp]

----

[[Documentation|Documentation index]]

@@ Line 6: / Line 6: @@
 ==Options==
   --pdbfile <pdbfile>  - PDB structure to analyze. Should have PDB format and CHARMM names for all atoms.
 Optional Parameters
   --outputpdbfile <outputpdbfile> - Creates a pdb file with the best(lowest energy) structure obtained. Should be specified for most applications.
   --logfile <logfile> - The output may be written to a text file. (Does not write the structure out. Prints the original and recovered values for chi dihedrals )
@@ Line 50: / Line 50: @@
 Optional - Num of rotamers per residue type (-ve or 0 means the wt rotamer alone will be used)
   --ALA <nALA>
   --ARG <nARG>
@@ Line 61: / Line 62: @@
 == Details ==
-The repack side chains program takes a pdb file and optimizes sidechain conformations.
+The repack side chains program takes a pdb file and optimizes all sidechain conformations.
 It uses discrete conformations from a rotamer library, and using state-of-the-art algorithms, repacks sidechains onto the input backbone structure.
@@ Line 70: / Line 71: @@
   > '''./repackSideChains --pdbfile 1A2J-for-repack-mini.pdb --rotlibfile rotlib-bonded_vdw_hb.txt --charmmtopfile top_all22_prot.inp --charmmparfile par_all22_prot.inp
     '''--hbondparfile canonical.inp --excludeenergyterm CHARMM_ELEC --printstats true --includecrystalrotamer true --ALA=-1 --GLY=-1 --PRO=-1 --outputpdbfile 1A2J_repacked.pdb
   ....

@@ Line 5: / Line 5: @@
 ==Options==
-  --pdbfile <pdbfile> PDB structure to analyze. Should have PDB format and CHARMM names for all atoms.
+  --pdbfile <pdbfile>  - PDB structure to analyze. Should have PDB format and CHARMM names for all atoms.
-  --rotlibfile <rotlibfile> RotamerLibrary file in MSL format.
+  --rotlibfile <rotlibfile> - RotamerLibrary file in MSL format.
-  --charmmtopfile <charmmTopFile> CHARMM Topology file.
+  --charmmtopfile <charmmTopFile> - CHARMM Topology file.
-  --charmmparfile <charmmParFile> CHARMM parameter file.
+  --charmmparfile <charmmParFile> - CHARMM parameter file.
-  --hbondparfile <hbondParFile> Hydrogen bond parameters file. [Example file in trunk./library/par_hbond_1.txt]
+  --hbondparfile <hbondParFile> - Hydrogen bond parameters file. [Example file in trunk/library/par_hbond_1.txt]
 Optional Parameters
-  --outputpdbfile <outputpdbfile> Creates a pdb file with the best(lowest energy) structure obtained. Shpuld be specified for most applications.
+  --outputpdbfile <outputpdbfile> - Creates a pdb file with the best(lowest energy) structure obtained. Should be specified for most applications.
-  --logfile <logfile> The output may be written to a text file. (Does not write the structure out)
+  --logfile <logfile> - The output may be written to a text file. (Does not write the structure out. Prints the original and recovered values for chi dihedrals )
-  --verbose <true/false> Prints additional information during the optimization process.
+  --verbose <true/false> - Prints additional information during the optimization process.
 Non bonded interactions - thresholds
@@ Line 21: / Line 21: @@
   --cutnb <nbcutnb> defaults to 11.0
-No interactions between atoms that are > cutnb apart are not considered at all.
+No interactions between atoms that are greater than cutnb Angstroms apart.
-All interactions between cutoff and cutnb have zero energy but the interactions are maintained by the CharmmSystemBuilder.
+All interactions at distances between cutoff and cutnb have zero energy but the interactions are maintained by the CharmmSystemBuilder.
 All interactions between cuton and cutoff are weighted using a switching function.
@@ Line 29: / Line 29: @@
   --configfile <configfile> All the options may be specified in a file.
-Algorithm
+Algorithms
   --rungoldsteinsingles <true/false> Defaults to true. Dead End Elimination using Goldstein Singles.
   --rungoldsteinpairs <true/false> Defaults to false. Dead End Elimination using Goldstein Pairs.
@@ Line 60: / Line 60: @@
 == Details ==
-repacking will ...
@@ Line 66: / Line 69: @@
   > '''./repackSideChains --pdbfile 1A2J-for-repack-mini.pdb --rotlibfile rotlib-bonded_vdw_hb.txt --charmmtopfile top_all22_prot.inp --charmmparfile par_all22_prot.inp
-    '''--hbondparfile canonical.inp --excludeenergyterm CHARMM_ELEC --printstats true --includecrystalrotamer true --ALA=-1 --GLY=-1 --PRO=-1 --outputpdbfile 1A2J_with_cr_except_elec
+    '''--hbondparfile canonical.inp --excludeenergyterm CHARMM_ELEC --printstats true --includecrystalrotamer true --ALA=-1 --GLY=-1 --PRO=-1 --outputpdbfile 1A2J_repacked.pdb
   ....

@@ Line 30: / Line 30: @@
 Algorithm
-  --rungoldsteinsingles <true/false>
+  --rungoldsteinsingles <true/false> Defaults to true. Dead End Elimination using Goldstein Singles.
-  --rungoldsteinpairs <true/false>
+  --rungoldsteinpairs <true/false> Defaults to false. Dead End Elimination using Goldstein Pairs.
-  --runscmf <true/false>
+  --runscmf <true/false> Defaults to true. Runs the Self Consistent Mean Field Algorithm.
-  --runscmfbiasedmc <true/false>
+  --runscmfbiasedmc <true/false>  Defaults to false. Runs a Biased Monte Carlo search using the SCMF probabilities.
-  --rununbiasedmc <true/false>
+  --rununbiasedmc <true/false> Defaults to true. Runs a Monte Carlo Simulated Annealing algorithm.
 Optional MC Parameters
@@ Line 46: / Line 44: @@
   --mcdeltasteps <numsteps>
   --mcmindeltaenergy <minEnergy>
 Optional - Num of rotamers per residue type (-ve or 0 means the wt rotamer alone will be used)

@@ Line 64: / Line 64: @@
   > '''./repackSideChains --pdbfile 1A2J-for-repack-mini.pdb --rotlibfile rotlib-bonded_vdw_hb.txt --charmmtopfile top_all22_prot.inp --charmmparfile par_all22_prot.inp
-    --hbondparfile canonical.inp --excludeenergyterm CHARMM_ELEC --printstats true --includecrystalrotamer true --ALA=-1 --GLY=-1 --PRO=-1 --outputpdbfile 1A2J_with_cr_except_elec'''
+    '''--hbondparfile canonical.inp --excludeenergyterm CHARMM_ELEC --printstats true --includecrystalrotamer true --ALA=-1 --GLY=-1 --PRO=-1 --outputpdbfile 1A2J_with_cr_except_elec
   ....

@@ Line 63: / Line 63: @@
 ==Examples==
-  > '''./repackSideChains --pdbfile 1A2J-for-repack-mini.pdb --rotlibfile rotlib-bonded_vdw_hb.txt --charmmtopfile top_all22_prot.inp --charmmparfile par_all22_prot.inp --hbondparfile canonical.inp --excludeenergyterm CHARMM_ELEC --printstats true --includecrystalrotamer true --ALA=-1 --GLY=-1 --PRO=-1 --outputpdbfile 1A2J_with_cr_except_elec'''
+  > '''./repackSideChains --pdbfile 1A2J-for-repack-mini.pdb --rotlibfile rotlib-bonded_vdw_hb.txt --charmmtopfile top_all22_prot.inp --charmmparfile par_all22_prot.inp
   ....

@@ Line 1: / Line 1: @@
 ==repackSideChains==
 A program to repack side chains of an input structure.
 ==Options==
-  --pdb      FILE.pdb    PDB structure to analyze
+  --pdbfile      FILE.pdb    PDB structure to analyze
@@ Line 14: / Line 14: @@
 ==Examples==
-  > '''repackSideChains --pdb ~/Downloads/1MEL.pdb'''
+  > '''./repackSideChains --pdbfile 1A2J-for-repack-mini.pdb --rotlibfile rotlib-bonded_vdw_hb.txt --charmmtopfile top_all22_prot.inp --charmmparfile par_all22_prot.inp --hbondparfile canonical.inp --excludeenergyterm CHARMM_ELEC --printstats true --includecrystalrotamer true --ALA=-1 --GLY=-1 --PRO=-1 --outputpdbfile 1A2J_with_cr_except_elec'''
- SOME OUTPUT HERE FOR 1MEL.pdb
   ....