MMTSB on Biowulf
The Multiscale Modeling Tools for Structural Biology (MMTSB) Tool Set is a novel set of utilities and programming libraries that provide new enhanced sampling and multiscale modeling techniques for the simulation of proteins and nucleic acids. The tool set interfaces with the existing molecular modeling packages CHARMM and Amber for classical all-atom simulations, and with MONSSTER for lattice-based low-resolution conformational sampling.
To set up the environment for MMTSB, use the 'module load MMTSB' command as in the example below.
biowulf% module load mmtsb
Integration with other packages
The MMTSB Tool Set benefits from the availability of other software packages, in particular CHARMM, Amber, NAMD, Modeller, DSSP, SCWRL, NCBI-BLAST, PSIPRED. Note that the Tool Set now works with installation of either scwrl3 or scwrl2.5.
Please contact staff@helix.nih.gov if you are interested in using MMTSB with SCWRL or MODELLER.
The following environment variables are related to these packages and should be set accordingly. The values below are suggestions: the version of the program often depends on the network (gige, ipath, ib) that you want to use.
| CHARMMEXEC | set to the specific executable you want to use. e.g. /usr/local/charmm/c35b2/gfortx86-xlg |
| CHARMMDATA | /usr/local/charmm/c35b2/toppar |
| AMBERHOME | /usr/local/amber |
| SANDEREXEC | /usr/local/amber/exe/sander.MPI |
| LEAPEXEC | /usr/local/amber/exe/tleap |
| NAMDEXEC | /usr/local/namd/2.7b2/x86_64/eth/namd2 |
| PSIPREDDIR | /usr/local/psipred |
| PDBDIR | /pdb/pdb |
Documentation
Documentation at the MMTSB website.
