MMTSB
Tool Set Documentation

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Structure preparation

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

Structure analysis

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)

SICHO Lattice Modeling

genchain.pl geninput.pl checkchain.pl genrestr.pl genseq.pl hlamc.pl latticeener.pl latticesim.pl rebuild.pl xtracttra.pl

Replica Exchange Sampling

aarex.pl aarexAmaber.pl latrex.pl gorex.pl hlamcrex.pl readArchive.pl rexanalysis.pl rexinfo.pl rexserver.pl writeArchive.pl



Ensemble Computing

bestcluster.pl calcprop.pl checkin.pl enscluster.pl enscut.pl enseval.pl ensfiles.pl enslatsim.pl ensmin.pl ensrun.pl getprop.pl showcluster.pl jobserver.pl setprop.pl


Structure Prediction

buildModel.pl psiblast.pl psipred.pl