MMTSB

From HP-SEE Wiki

• Web site: http://www.mmtsb.org also here
• Described version: NA
• Licensing: Freely available for academic use License
• User documentation: http://blue11.bch.msu.edu/mmtsb/Main_Page
• Download: http://mmtsb.org/cgi-bin/download?toolset
• Source code: http://mmtsb.org/cgi-bin/download?toolset

Authors/Maintainers

http://www.mmtsb.org/people.html

Primary citations:

• Michael Feig, John Karanicolas, Charles L. Brooks, III: MMTSB Tool Set (2001), MMTSB NIH Research Resource, The Scripps Research Institute
• Michael Feig, John Karanicolas, Charles L. Brooks III: MMTSB Tool Set: Enhanced Sampling and Multiscale Modeling Methods for Applications in Structural Biology, Journal of Molecular Graphics and Modeling (2004) 22, 377-395

Summary

Multiscale Modeling Tools for Structural Biology (MMTSB) Tool Set is a 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. MMTSB integrates the existing programs through an interface layer while providing missing functionality as necessary. It uses Perl interpreted scripting language, which combines ease of use and portability with a high level of functionality for addressing the complex system-oriented but computationally less intensive tasks. The functionalities that are provided through MMTSB focus on energy evaluations, minimization and molecular dynamics runs. Input structures are in PDB format, with necessary name and format conversions done automatically and transparently for standard protein structures. Manual PDB format translations can be made through convpdb.pl special utility which can do a variety of manipulations that may involve changing residue numbering, editing chain identifiers, translating coordinates and sub- selecting or merging structure fragments. MMTSB can be used in scoring of previously generated protein conformations with the ensemble computing facility, folding of peptides via replica exchange simulations, and the prediction of a missing fragment in the context of a known structure.

Features

• Listed features

Architectural/Functional Overview

• high level design info, how it works, performance - may be a link, or several links

Usage Overview

Tutorial

Usage within ISyMAB

Dependacies

• GNU compilers
• Perl
• CHARMM
• NAMD

HP-SEE Applications

• ISyMAB

Resource Centers

• IFIN_BIO, RO

Usage by Other Projects and Communities

• If any

Recommendations for Configuration and Usage

Please describe here any common settings, configurations or conventions that would make the usage of this resource (library or tool) more interoperable or scalable across the HP-SEE resources. These recommendations should include anything that is related to the resource and is agreed upon by administrators and users, or across sites and applications. These recommendations should emerge from questions or discussions opened by site administrators or application developers, at any stage, including installation, development, usage, or adaptation for another HPC centre.

Provided descriptions should describe general or site specific aspects of resource installation, configuration and usage, or describe the guidelines or convention for deploying or using the resource within the local (user/site) or temporary environment (job). Examples are:

• Common configuration settings of execution environment
• Filesystem path or local access string
• Environment variables to be set or used by applications
• Options (e.g. additional modules) that are needed or required by applications and should be present
• Minimum quantitative values (e.g. quotas) offered by the site
• Location and format of some configuration or usage hint instructing applications on proper use of the resource or site specific policy
• Key installation or configuration settings that should be set to a common value, or locally tweaked by local site admins
• Conventions for application or job bound installation and usage of the resource