How can I use the General Amber Force Field (GAFF) in Desmond?

To generate Desmond readable files using GAFF, use the following steps:

1) Use antechamber and tleap to generate AMBER prmtop and prmcrd files. antechamber and tleap programs are distributed free with the new amber tools (http://ambermd.org/#AmberTools).

2) Use the Python script amber_prm2cms.py to convert the amber format files to Desmond readable input. Usage:

$SCHRODINGER/run amber_prm2cms.py -p prmtop -c prmcrd -o output.cms

Keywords: Desmond, GAFF, force field, Amber

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