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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
| 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 |
| psipred.pl | predict secondary structure with PSIPRED |
| psiblast.pl | obtain sequence alignment with PSI-BLAST |