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Some collected tools for molecular simulation pipelines
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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.