|
Main Page
From MMTSB
Common applications of the MMTSB toolset
Helpful hints for using the MMTSB toolset in projects
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
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
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 |
psipred.pl | predict secondary structure with PSIPRED |
psiblast.pl | obtain sequence alignment with PSI-BLAST |