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MSMS

Quick instructions for installing the msms program for molecular surface calculations.
Note:
We have marked the MSMS interface (msms.py) as 'OLD' -- that means it is there and should work but we currently prefer and support SurfaceRacer for the same task.
  1. download the msms binary

    from http://mgltools.scripps.edu/downloads or:

    cd /tmp/
    wget http://mgltools.scripps.edu/downloads/tars/releases/MSMSRELEASE/REL2.6.1/msms_i86Linux2_2.6.1.tar.gz
    

    Note:

    Some of the msms scripts (used by biskit) require the gawk program. Make sure it is installed. See MSMS troubleshooting

  2. Unpack into new directory:

    sudo mkdir /usr/local/lib/msms
    cd /usr/local/lib/msms
    sudo tar zxvf /tmp/msms_i86Linux2_2.6.1.tar.gz
    
  3. Link/Copy executables into your $PATH:

    sudo ln -s /usr/local/lib/msms/msms.i86Linux2.2.6.1 /usr/local/bin/msms
    sudo ln -s /usr/local/lib/msms/pdb_to_xyzr* /usr/local/bin
    
  4. Test Biskit interface:

    cd biskit/Biskit
    python msms.py
    

    Problems? See MSMS troubleshooting!


Usage:
see msms.py
Custom configuration:
  • biskit/external/defaults/exe_msms.dat
  • biskit/external/defaults/exe_pdb2xyzrn.dat