MSL-Libraries - User contributions [en]

MSL Programs::repackSideChains

2011-11-22T05:34:20Z

Sab:

==repackSideChains==

A program to repack side chains of an input structure.

==Options==
--pdbfile <pdbfile> - PDB structure to analyze. Should have PDB format and CHARMM names for all atoms.
--rotlibfile <rotlibfile> - RotamerLibrary file in MSL format.
--charmmtopfile <charmmTopFile> - CHARMM Topology file.
--charmmparfile <charmmParFile> - CHARMM parameter file.
--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. 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 )
--verbose <true/false> - Prints additional information during the optimization process.

Non bonded interactions - thresholds
--cuton <nbcuton> defaults to 9.0
--cutoff <nbcutoff> defaults to 10.0
--cutnb <nbcutnb> defaults to 11.0

No interactions between atoms that are greater than cutnb Angstroms apart.
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.

--includecrystalrotamer <true/false> Specify if crystal rotamer should be considered during repack. Should be set to false(defaults to false) to evaluate sidechain recovery.
--configfile <configfile> All the options may be specified in a file.

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.
--runscmf <true/false> Defaults to true. Runs the Self Consistent Mean Field Algorithm.
--runscmfbiasedmc <true/false> Defaults to false. Runs a Biased Monte Carlo search using the SCMF probabilities.
--rununbiasedmc <true/false> Defaults to true. Runs a Monte Carlo Simulated Annealing algorithm.

Optional MC Parameters
--mcstarttemp <startT>
--mcendtemp <endT>
--mccycles <numCycles>
--mcshape <CONSTANT/LINEAR/EXPONENTIAL/SIGMOIDAL/SOFT>
--mcmaxreject <numReject>
--mcdeltasteps <numsteps>
--mcmindeltaenergy <minEnergy>

--excludeenergyterm <term1> --excludeenergyterm <term2>
[Terms can be CHARMM_ANGL,CHARMM_BOND,CHARMM_DIHE,CHARMM_ELEC,CHARMM_IMPR,CHARMM_U-BR,CHARMM_VDW,SCWRL4_HBOND] All terms are implemented by default

Optional - Num of rotamers per residue type (-ve or 0 means the wt rotamer alone will be used)
--ALA <nALA>
--ARG <nARG>
.........
--HSD <nHSD>
--HSE <nHSD>
--HSP <nHSP>
.......
--VAL <nVAL>

== Details ==

The repack side chains program takes a pdb file and optimizes sidechain conformations.
It uses discrete conformations from a rotamer library, and using state-of-the-art algorithms, repacks sidechains onto the input backbone structure.

==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_repacked.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]]

MSL Programs::repackSideChains

2011-11-21T23:21:54Z

Sab: /* Options */

==repackSideChains==

A program to repack side chains of an input structure.

==Options==
--pdbfile <pdbfile> PDB structure to analyze. Should have PDB format and CHARMM names for all atoms.
--rotlibfile <rotlibfile> RotamerLibrary file in MSL format.
--charmmtopfile <charmmTopFile> CHARMM Topology file.
--charmmparfile <charmmParFile> CHARMM parameter file.
--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.
--logfile <logfile> The output may be written to a text file. (Does not write the structure out)
--verbose <true/false> Prints additional information during the optimization process.

Non bonded interactions - thresholds
--cuton <nbcuton> defaults to 9.0
--cutoff <nbcutoff> defaults to 10.0
--cutnb <nbcutnb> defaults to 11.0

No interactions between atoms that are > cutnb apart are not considered at all.
All interactions 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.

--includecrystalrotamer <true/false> Specify if crystal rotamer should be considered during repack. Should be set to false(defaults to false) to evaluate sidechain recovery.
--configfile <configfile> All the options may be specified in a file.

Algorithm
--rungoldsteinsingles <true/false> Defaults to true. Dead End Elimination using Goldstein Singles.
--rungoldsteinpairs <true/false> Defaults to false. Dead End Elimination using Goldstein Pairs.
--runscmf <true/false> Defaults to true. Runs the Self Consistent Mean Field Algorithm.
--runscmfbiasedmc <true/false> Defaults to false. Runs a Biased Monte Carlo search using the SCMF probabilities.
--rununbiasedmc <true/false> Defaults to true. Runs a Monte Carlo Simulated Annealing algorithm.

Optional MC Parameters
--mcstarttemp <startT>
--mcendtemp <endT>
--mccycles <numCycles>
--mcshape <CONSTANT/LINEAR/EXPONENTIAL/SIGMOIDAL/SOFT>
--mcmaxreject <numReject>
--mcdeltasteps <numsteps>
--mcmindeltaenergy <minEnergy>

--excludeenergyterm <term1> --excludeenergyterm <term2>
[Terms can be CHARMM_ANGL,CHARMM_BOND,CHARMM_DIHE,CHARMM_ELEC,CHARMM_IMPR,CHARMM_U-BR,CHARMM_VDW,SCWRL4_HBOND] All terms are implemented by default

Optional - Num of rotamers per residue type (-ve or 0 means the wt rotamer alone will be used)
--ALA <nALA>
--ARG <nARG>
.........
--HSD <nHSD>
--HSE <nHSD>
--HSP <nHSP>
.......
--VAL <nVAL>

== Details ==
repacking will ...

==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

....

==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]]

MSL Programs::repackSideChains

2011-11-21T22:56:40Z

Sab: /* Examples */

==repackSideChains==

A program to repack side chains of an input structure.

==Options==
--pdbfile <pdbfile> PDB structure to analyze. Should have PDB format and CHARMM names for all atoms.
--rotlibfile <rotlibfile> RotamerLibrary file in MSL format.
--charmmtopfile <charmmTopFile> CHARMM Topology file.
--charmmparfile <charmmParFile> CHARMM parameter file.
--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.
--logfile <logfile> The output may be written to a text file. (Does not write the structure out)
--verbose <true/false> Prints additional information during the optimization process.

Non bonded interactions - thresholds
--cuton <nbcuton> defaults to 9.0
--cutoff <nbcutoff> defaults to 10.0
--cutnb <nbcutnb> defaults to 11.0

No interactions between atoms that are > cutnb apart are not considered at all.
All interactions 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.

--includecrystalrotamer <true/false> Specify if crystal rotamer should be considered during repack. Should be set to false(defaults to false) to evaluate sidechain recovery.
--configfile <configfile> All the options may be specified in a file.

Algorithm
--rungoldsteinsingles <true/false>
--rungoldsteinpairs <true/false>
--runscmf <true/false>
--runscmfbiasedmc <true/false>
--rununbiasedmc <true/false>
--excludeenergyterm <term1> --excludeenergyterm <term2>
[Terms can be CHARMM_ANGL,CHARMM_BOND,CHARMM_DIHE,CHARMM_ELEC,CHARMM_IMPR,CHARMM_U-BR,CHARMM_VDW,SCWRL4_HBOND] All terms are implemented by default

Optional MC Parameters
--mcstarttemp <startT>
--mcendtemp <endT>
--mccycles <numCycles>
--mcshape <CONSTANT/LINEAR/EXPONENTIAL/SIGMOIDAL/SOFT>
--mcmaxreject <numReject>
--mcdeltasteps <numsteps>
--mcmindeltaenergy <minEnergy>

Optional - Num of rotamers per residue type (-ve or 0 means the wt rotamer alone will be used)
--ALA <nALA>
--ARG <nARG>
.........
--HSD <nHSD>
--HSE <nHSD>
--HSP <nHSP>
.......
--VAL <nVAL>

== Details ==
repacking will ...

==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

....

==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]]

MSL Programs::repackSideChains

2011-11-21T22:56:21Z

Sab: /* Examples */

==repackSideChains==

A program to repack side chains of an input structure.

==Options==
--pdbfile <pdbfile> PDB structure to analyze. Should have PDB format and CHARMM names for all atoms.
--rotlibfile <rotlibfile> RotamerLibrary file in MSL format.
--charmmtopfile <charmmTopFile> CHARMM Topology file.
--charmmparfile <charmmParFile> CHARMM parameter file.
--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.
--logfile <logfile> The output may be written to a text file. (Does not write the structure out)
--verbose <true/false> Prints additional information during the optimization process.

Non bonded interactions - thresholds
--cuton <nbcuton> defaults to 9.0
--cutoff <nbcutoff> defaults to 10.0
--cutnb <nbcutnb> defaults to 11.0

No interactions between atoms that are > cutnb apart are not considered at all.
All interactions 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.

--includecrystalrotamer <true/false> Specify if crystal rotamer should be considered during repack. Should be set to false(defaults to false) to evaluate sidechain recovery.
--configfile <configfile> All the options may be specified in a file.

Algorithm
--rungoldsteinsingles <true/false>
--rungoldsteinpairs <true/false>
--runscmf <true/false>
--runscmfbiasedmc <true/false>
--rununbiasedmc <true/false>
--excludeenergyterm <term1> --excludeenergyterm <term2>
[Terms can be CHARMM_ANGL,CHARMM_BOND,CHARMM_DIHE,CHARMM_ELEC,CHARMM_IMPR,CHARMM_U-BR,CHARMM_VDW,SCWRL4_HBOND] All terms are implemented by default

Optional MC Parameters
--mcstarttemp <startT>
--mcendtemp <endT>
--mccycles <numCycles>
--mcshape <CONSTANT/LINEAR/EXPONENTIAL/SIGMOIDAL/SOFT>
--mcmaxreject <numReject>
--mcdeltasteps <numsteps>
--mcmindeltaenergy <minEnergy>

Optional - Num of rotamers per residue type (-ve or 0 means the wt rotamer alone will be used)
--ALA <nALA>
--ARG <nARG>
.........
--HSD <nHSD>
--HSE <nHSD>
--HSP <nHSP>
.......
--VAL <nVAL>

== Details ==
repacking will ...

==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'''

....

==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]]

MSL Programs::repackSideChains

2011-11-21T22:55:38Z

Sab: /* Options */

==repackSideChains==

A program to repack side chains of an input structure.

==Options==
--pdbfile <pdbfile> PDB structure to analyze. Should have PDB format and CHARMM names for all atoms.
--rotlibfile <rotlibfile> RotamerLibrary file in MSL format.
--charmmtopfile <charmmTopFile> CHARMM Topology file.
--charmmparfile <charmmParFile> CHARMM parameter file.
--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.
--logfile <logfile> The output may be written to a text file. (Does not write the structure out)
--verbose <true/false> Prints additional information during the optimization process.

Non bonded interactions - thresholds
--cuton <nbcuton> defaults to 9.0
--cutoff <nbcutoff> defaults to 10.0
--cutnb <nbcutnb> defaults to 11.0

No interactions between atoms that are > cutnb apart are not considered at all.
All interactions 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.

--includecrystalrotamer <true/false> Specify if crystal rotamer should be considered during repack. Should be set to false(defaults to false) to evaluate sidechain recovery.
--configfile <configfile> All the options may be specified in a file.

Algorithm
--rungoldsteinsingles <true/false>
--rungoldsteinpairs <true/false>
--runscmf <true/false>
--runscmfbiasedmc <true/false>
--rununbiasedmc <true/false>
--excludeenergyterm <term1> --excludeenergyterm <term2>
[Terms can be CHARMM_ANGL,CHARMM_BOND,CHARMM_DIHE,CHARMM_ELEC,CHARMM_IMPR,CHARMM_U-BR,CHARMM_VDW,SCWRL4_HBOND] All terms are implemented by default

Optional MC Parameters
--mcstarttemp <startT>
--mcendtemp <endT>
--mccycles <numCycles>
--mcshape <CONSTANT/LINEAR/EXPONENTIAL/SIGMOIDAL/SOFT>
--mcmaxreject <numReject>
--mcdeltasteps <numsteps>
--mcmindeltaenergy <minEnergy>

Optional - Num of rotamers per residue type (-ve or 0 means the wt rotamer alone will be used)
--ALA <nALA>
--ARG <nARG>
.........
--HSD <nHSD>
--HSE <nHSD>
--HSP <nHSP>
.......
--VAL <nVAL>

== Details ==
repacking will ...

==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'''

....

==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]]