Difference between revisions of "MSL Programs::repackSideChains"
From MSL-Libraries
Jump to navigationJump to search (→Options) |
|||
| Line 5: | Line 5: | ||
==Options== | ==Options== | ||
| − | --pdbfile | + | --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 == | == Details == | ||
Revision as of 22:55, 21 November 2011
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
....
