MMTSB
Tool Set Documentation

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__NOTOC__
 
__NOTOC__
 +
 +
MMTSB is now available on [https://github.com/mmtsb/toolset github]. Download with:
 +
 +
  git clone https://github.com/mmtsb/toolset.git
 +
 +
=== [[Common applications of the MMTSB toolset]] ===
 +
 +
=== [[Helpful hints for using the MMTSB toolset in projects]] ===
 +
 +
= Commands =
 
== Structure preparation ==
 
== Structure preparation ==
 
{|
 
{|
 
|-
 
|-
−
| <TT>[[convpdb.pl]]</TT>  || (conversion/manipulation of PDB files)
+
|width=200pt| <TT>[[convpdb.pl]]</TT>  || conversion/manipulation of PDB files
 
|-
 
|-
−
| <TT>[[complete.pl]]</TT> || (completion of missing atoms)
+
| <TT>[[complete.pl]]</TT> || completion of missing atoms
 
|-
 
|-
−
| <TT>[[mutate.pl]]</TT>  || (amino acid residue mutations)
+
| <TT>[[mutate.pl]]</TT>  || amino acid residue mutations
 
|-
 
|-
−
| <TT>[[mutateNA.pl]]</TT> || (nucleotide mutations)
+
| <TT>[[mutateNA.pl]]</TT> || nucleotide base mutations
 
|}
 
|}
  
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{|
 
{|
 
|-
 
|-
−
| <TT>[[centerOfMass.pl]]</TT> || (center of mass)
+
|width=200pt| <TT>[[analyze.pl]]</TT> || center of mass
 +
|-
 +
| <TT>[[centerOfMass.pl]]</TT> || center of mass
 
|-
 
|-
−
| <TT>[[rgyr.pl]]</TT> || (radius of gyration)
+
| <TT>[[rgyr.pl]]</TT> || radius of gyration
 
|-
 
|-
−
| <TT>[[rms.pl]]</TT>  || (root mean square displacement)
+
| <TT>[[rms.pl]]</TT>  || root mean square displacement
 
|-
 
|-
−
| <TT>[[lsqfit.pl]]</TT> || (least-squares fit superposition)
+
| <TT>[[lsqfit.pl]]</TT> || least-squares fit superposition
 
|-
 
|-
−
| <TT>[[contact.pl]]</TT> || (identification and comparison of native contacts)
+
| <TT>[[contact.pl]]</TT> || identification and comparison of native contacts
 
|-
 
|-
−
| <TT>[[countIntCont.pl]]</TT> || (contacts between different chains)
+
| <TT>[[countIntCont.pl]]</TT> || contacts between different chains
 
|-
 
|-
−
| <TT>[[mindist.pl]]</TT> || (minimum distance between two residues)
+
| <TT>[[mindist.pl]]</TT> || minimum distance between two residues
 
|-
 
|-
−
| <TT>[[qscore.pl]]</TT> || (Q-score calculation)
+
| <TT>[[qscore.pl]]</TT> || Q-score calculation
 
|-
 
|-
−
| <TT>[[dihed.pl]]</TT> || (phi/psi/chi1 dihedral calculation)
+
| <TT>[[dihed.pl]]</TT> || phi/psi/chi1 dihedral calculation
 
|-
 
|-
−
| <TT>[[vicinity.pl]]</TT> || (identification of residues within cutoff)
+
| <TT>[[vicinity.pl]]</TT> || identification of residues within cutoff
 
|-  
 
|-  
−
| <TT>[[cluster.pl]]</TT> || (clustering based on mutual similarity)
+
| <TT>[[cluster.pl]]</TT> || clustering based on mutual similarity
 
|}
 
|}
  
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{|
 
{|
 
|-
 
|-
−
| <TT>[[enerCHARMM.pl]]</TT> || (evaluate energy with CHARMM)
+
|width=200pt| <TT>[[enerCHARMM.pl]]</TT> || evaluate energy with CHARMM
 
|-
 
|-
−
| <TT>[[minCHARMM.pl]]</TT> || (minimize with CHARMM)
+
| <TT>[[minCHARMM.pl]]</TT> || minimize with CHARMM
 
|-
 
|-
−
| <TT>[[mdCHARMM.pl]]</TT>  || (run molecular dynamics with CHARMM)
+
| <TT>[[mdCHARMM.pl]]</TT>  || run molecular dynamics with CHARMM
 
|-
 
|-
−
| <TT>[[analyzeCHARMM.pl]]</TT> || (analyze molecular dynamics simulations with CHARMM)
+
| <TT>[[analyzeCHARMM.pl]]</TT> || analyze molecular dynamics simulations with CHARMM
 
|-
 
|-
−
| <TT>[[nmaCHARMM.pl]]</TT> || (normal mode analysis with CHARMM)
+
| <TT>[[nmaCHARMM.pl]]</TT> || normal mode analysis with CHARMM
 
|-
 
|-
−
| <TT>[[pbCHARMM.pl]]</TT> || (Poisson-Boltzmann calculations with CHARMM)
+
| <TT>[[pbCHARMM.pl]]</TT> || Poisson-Boltzmann calculations with CHARMM
 
|-
 
|-
−
| <TT>[[equiCHARMM.pl]]</TT> || (explicit solvent simulations equilibration)
+
| <TT>[[equiCHARMM.pl]]</TT> || explicit solvent simulations equilibration
 
|-
 
|-
−
| <TT>[[scalarCHARMM.pl]]</TT> || (obtain scalar variables from CHARMM)
+
| <TT>[[scalarCHARMM.pl]]</TT> || obtain scalar variables from CHARMM
 
|-
 
|-
−
| <TT>[[genPSF.pl]]</TT> || (generate PSF file from PDB)
+
| <TT>[[genPSF.pl]]</TT> || generate PSF file from PDB
 
|-
 
|-
−
| <TT>[[pdb2traj.pl]]</TT> || (generate DCD trajectory from list of PDBs)
+
| <TT>[[pdb2traj.pl]]</TT> || generate DCD trajectory from list of PDBs
 
|-  
 
|-  
−
| <TT>[[processDCD.pl]]</TT> || (process DCD trajectory file)
+
| <TT>[[processDCD.pl]]</TT> || process DCD trajectory file
 +
|-
 +
| <TT>[[enerAmber.pl]]</TT>  || evaluate energy with Amber
 
|-
 
|-
−
| <TT>[[enerAmber.pl]]</TT> || (evaluate energy with Amber)
+
| <TT>[[minAmber.pl]]</TT> || minimize with Amber
 
|-
 
|-
−
| <TT>[[minAmber.pl]]</TT> || (minimize with Amber)
+
| <TT>[[mdAmber.pl]]</TT>   || run molecular dynamics simulation with Amber
 
|-
 
|-
−
| <TT>[[mdAmber.pl]]</TT>  || (run molecular dynamics simulation with Amber)
+
| <TT>[[mdNAMD.pl]]</TT>  || run molecular dynamics simulation with NAMD
 
|}
 
|}
  
 
== SICHO Lattice Modeling ==
 
== SICHO Lattice Modeling ==
  
−
genchain.pl
+
{|
−
geninput.pl
+
|-
−
checkchain.pl
+
|width=200pt| <TT>[[latticesim.pl]]</TT> || SICHO lattice simulation with MONSSTER
−
genrestr.pl
+
|-
−
genseq.pl
+
| <TT>[[latticeener.pl]]</TT> || SICHO energy from MONSSTER
−
hlamc.pl
+
|-
−
latticeener.pl
+
| <TT>[[genchain.pl]]</TT>  || generate lattice chain from PDB
−
latticesim.pl
+
|-
−
rebuild.pl
+
| <TT>[[rebuild.pl]]</TT> || rebuild all-atom model from lattice chain
−
xtracttra.pl
+
|-
 +
| <TT>[[checkchain.pl]]</TT> || check validity of lattice chain
 +
|-
 +
| <TT>[[genseq.pl]]</TT> || generate MONSSTER sequence file
 +
|-
 +
| <TT>[[geninput.pl]]</TT> || generate MONSSTER input file
 +
|-
 +
| <TT>[[genrestr.pl]]</TT> || generate MONSSTER restraint file
 +
|-
 +
| <TT>[[xtracttra.pl]]</TT> || extract lattice chain from MONSSTER trajectory
 +
|-
 +
| <TT>[[hlamc.pl]]</TT> || multi-scale lattice/all-atom sampling
 +
|}
  
 
== Replica Exchange Sampling ==
 
== Replica Exchange Sampling ==
  
−
aarex.pl
+
{|
−
aarexAmaber.pl
+
|-
−
latrex.pl
+
|width=200pt| <TT>[[aarex.pl]]</TT> || all-atom replica exchange simulation with CHARMM
−
gorex.pl
+
|-
−
hlamcrex.pl
+
| <TT>[[aarexAmber.pl]]</TT> || all-atom replica exchange simulation with Amber
−
readArchive.pl
+
|-
−
rexanalysis.pl
+
| <TT>[[latrex.pl]]</TT>  || lattice replica exchange simulation with MONSSTER
−
rexinfo.pl
+
|-
−
rexserver.pl
+
| <TT>[[gorex.pl]]</TT> || GO model replica exchange simulation with CHARMM
−
writeArchive.pl
+
|-
−
 
+
| <TT>[[hlamcrex.pl]]</TT> || multi-scale lattice/all-atom replica exchange simulation)
−
 
+
|-
−
 
+
| <TT>[[rexinfo.pl]]</TT> || replica exchange control information
 +
|-
 +
| <TT>[[rexanalysis.pl]]</TT> || replica exchange analysis
 +
|-
 +
| <TT>[[readArchive.pl]]</TT> || read replica exchange trajectory archive file
 +
|-
 +
| <TT>[[writeArchive.pl]]</TT> || write replica exchange trajectory archive file
 +
|-
 +
| <TT>[[rexserver.pl]]</TT> || replica exchange server
 +
|}
  
 
== Ensemble Computing ==
 
== Ensemble Computing ==
−
bestcluster.pl
+
{|
−
calcprop.pl
+
|-
−
checkin.pl
+
|width=200pt| <TT>[[checkin.pl]]</TT> || generate ensemble from PDB files
−
enscluster.pl
+
|-
−
enscut.pl
+
| <TT>[[ensrun.pl]]</TT> || run command across ensemble
−
enseval.pl
+
|-
−
ensfiles.pl
+
| <TT>[[ensmin.pl]]</TT>  || minimize ensemble structures
−
enslatsim.pl
+
|-
−
ensmin.pl
+
| <TT>[[enseval.pl]]</TT> || evaluate energy for members of ensemble
−
ensrun.pl
+
|-
−
getprop.pl
+
| <TT>[[enslatsim.pl]]</TT> || generate ensemble from lattice simulations
−
showcluster.pl
+
|-
−
jobserver.pl
+
| <TT>[[enscut.pl]]</TT> || truncate residues of all members of ensemble
−
setprop.pl
+
|-
−
 
+
| <TT>[[ensfiles.pl]]</TT> || obtain list of files for ensemble structures
 +
|-
 +
| <TT>[[getprop.pl]]</TT> || obtain data items for ensemble structures
 +
|-
 +
| <TT>[[setprop.pl]]</TT> || set data items for ensemble structures
 +
|-
 +
| <TT>[[calcprop.pl]]</TT> || calculate standard structural properties for ensemble
 +
|-
 +
| <TT>[[enscluster.pl]]</TT> || cluster ensemble structures
 +
|-
 +
| <TT>[[bestcluster.pl]]</TT>  || rank clusters
 +
|-
 +
| <TT>[[showcluster.pl]]</TT> || display clusters
 +
|-
 +
| <TT>[[jobserver.pl]]</TT>  || start job server for parallel runs
 +
|}
  
 
== Structure Prediction ==
 
== Structure Prediction ==
−
 
+
{|
−
buildModel.pl
+
|-
−
psiblast.pl
+
|width=200pt| <TT>[[buildModel.pl]]</TT> || build template-based model with loops generated by MODELLER
−
psipred.pl
+
|-
 +
| <TT>[[loopModel.pl]]</TT> || model loops with MODELLER
 +
|-
 +
| <TT>[[psipred.pl]]</TT> || predict secondary structure with PSIPRED
 +
|-
 +
| <TT>[[psiblast.pl]]</TT>  || obtain sequence alignment with PSI-BLAST
 +
|}

Latest revision as of 17:46, 17 December 2016


MMTSB is now available on github. Download with: 

 git clone https://github.com/mmtsb/toolset.git

Common applications of the MMTSB toolset

Helpful hints for using the MMTSB toolset in projects

Commands

Structure preparation

convpdb.pl conversion/manipulation of PDB files
complete.pl completion of missing atoms
mutate.pl amino acid residue mutations
mutateNA.pl nucleotide base mutations

Structure analysis

analyze.pl center of mass
centerOfMass.pl center of mass
rgyr.pl radius of gyration
rms.pl root mean square displacement
lsqfit.pl least-squares fit superposition
contact.pl identification and comparison of native contacts
countIntCont.pl contacts between different chains
mindist.pl minimum distance between two residues
qscore.pl Q-score calculation
dihed.pl phi/psi/chi1 dihedral calculation
vicinity.pl identification of residues within cutoff
cluster.pl clustering based on mutual similarity

All-Atom Modeling

enerCHARMM.pl evaluate energy with CHARMM
minCHARMM.pl minimize with CHARMM
mdCHARMM.pl run molecular dynamics with CHARMM
analyzeCHARMM.pl analyze molecular dynamics simulations with CHARMM
nmaCHARMM.pl normal mode analysis with CHARMM
pbCHARMM.pl Poisson-Boltzmann calculations with CHARMM
equiCHARMM.pl explicit solvent simulations equilibration
scalarCHARMM.pl obtain scalar variables from CHARMM
genPSF.pl generate PSF file from PDB
pdb2traj.pl generate DCD trajectory from list of PDBs
processDCD.pl process DCD trajectory file
enerAmber.pl evaluate energy with Amber
minAmber.pl minimize with Amber
mdAmber.pl run molecular dynamics simulation with Amber
mdNAMD.pl run molecular dynamics simulation with NAMD

SICHO Lattice Modeling

latticesim.pl SICHO lattice simulation with MONSSTER
latticeener.pl SICHO energy from MONSSTER
genchain.pl generate lattice chain from PDB
rebuild.pl rebuild all-atom model from lattice chain
checkchain.pl check validity of lattice chain
genseq.pl generate MONSSTER sequence file
geninput.pl generate MONSSTER input file
genrestr.pl generate MONSSTER restraint file
xtracttra.pl extract lattice chain from MONSSTER trajectory
hlamc.pl multi-scale lattice/all-atom sampling

Replica Exchange Sampling

aarex.pl all-atom replica exchange simulation with CHARMM
aarexAmber.pl all-atom replica exchange simulation with Amber
latrex.pl lattice replica exchange simulation with MONSSTER
gorex.pl GO model replica exchange simulation with CHARMM
hlamcrex.pl multi-scale lattice/all-atom replica exchange simulation)
rexinfo.pl replica exchange control information
rexanalysis.pl replica exchange analysis
readArchive.pl read replica exchange trajectory archive file
writeArchive.pl write replica exchange trajectory archive file
rexserver.pl replica exchange server

Ensemble Computing

checkin.pl generate ensemble from PDB files
ensrun.pl run command across ensemble
ensmin.pl minimize ensemble structures
enseval.pl evaluate energy for members of ensemble
enslatsim.pl generate ensemble from lattice simulations
enscut.pl truncate residues of all members of ensemble
ensfiles.pl obtain list of files for ensemble structures
getprop.pl obtain data items for ensemble structures
setprop.pl set data items for ensemble structures
calcprop.pl calculate standard structural properties for ensemble
enscluster.pl cluster ensemble structures
bestcluster.pl rank clusters
showcluster.pl display clusters
jobserver.pl start job server for parallel runs

Structure Prediction

buildModel.pl build template-based model with loops generated by MODELLER
loopModel.pl model loops with MODELLER
psipred.pl predict secondary structure with PSIPRED
psiblast.pl obtain sequence alignment with PSI-BLAST
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