Article ID: 300 - Last Modified: December 4, 2010
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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