Some collected tools for molecular simulation pipelines
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DatabaseTopology
OLDTopology/Topology
ambertools
converters
ctools
examples
gromacstools
mccetools
modellertools
moltools
packmoltools
pdbtools
pipelinetools
relativetools
utilities
README
__init__.py

README

README for mmtools
Last updated: August 12, 2008 by Vincent Voelz


INSTALLATION

Downloading mmtools from the svn repository

mmtools is a SimBios project, found at simtk.org. You need to be added to the Simbios project through a request via SimBios.
See: https://simtk.org/home/mmtools

One of the following people should be able to add you as a project member. Current team members (as of October 2007):

    * Vincent Voelz
    * David Mobley
    * John Chodera
    * Greg Bowman
    * Imran Haque
    * Guha
    * Peter? 

Once you've been added to the Simbios project, you should be able to check out the svn repository. 
You will need to have svn installed. To checkout the repository, cd to a directory in which you
want to install mmtools, and use:

>> svn checkout --username <your_SVN_name> https://simtk.org/svn/mmtools


REQUIREMENTS

# Requirements for gromacstools:
#
#    1) GROMACS ( http://www.gromacs.org/ ) must be installed on your machine, 
#       and the following Environment variables must be defined (in your .bash_profile, e.g.):
# 
#        GMXLIB             the pathname of the gmx parameter files.  
#        GMXPATH            the pathname of the Gromacs executables  (This also needs to be in your PATH)
#        GMXPATH_PS3        the pathname of the Gromacs executables used for building PlayStation3 WUs
#        MMTOOLSPATH        the pathname of the mmtools library
#
#    2) The AMBER ports for GROMACS ( http://folding.stanford.edu/ffamber/ ) by Sorin, Park
#       and Pande must be installed, with the *.itp, *.rtp, etc., files in the $GMXLIB directory (.../share/top )
#
#    3) If you need to simulate any proteins with a norleucine (NLE) residue, you will need to insert the
#       following lines in the *.hdb and *.rtp files for the ffamber gmx port forcefields:
#
#           ffamber/norleucine.hdb
#           ffamber/norleucine.rtp


DESCRIPTION

Various tools useful for the the setup and analysis of molecular simulations of biomolecules.

* ambertools

Tools for interacting with programs from the AMBER molecular mechanics package, including Antechamber for the parameterization of small molecules using GAFF.

* converters

Various converters for converting systems between molecular mechanics packages, especially acpypi (available from Google Code) and amb2gmx.pl (obsolete, replaced by acpypi)

* gromacstools

Tools for interacting with the gromacs molecular mechanics package.

* mccetools

Tools for interacting with MCCE/Delphi for the selection of likely protonation states or pKa estimation.

* modellertools

Tools for modeling proteins from sequence and homologous structure.  Also useful for building in missing heavy atoms or residues in X-ray structures.

* moltools

Tools for dealing with small molecules.
Requires the OEChem library from OpenEye.

* utility

Various utility classes with physical constants, units, etc.

* pdbtools

Some tools for performing common operations on PDB files

GITHUB MIGRATION

Because of 50M desired filesize limitations, all .cms files were gzipped.