Hi AMBER experts,
I am trying to solvate a molecular triad in a benzonitrile box. For this molecular triad, I used Antechamber to generate the topology file with GAFF. The charge is calculated using AM1-BCC. I have done some literature search and I found OPLS force filed has the parameters for benzonitrile. Is it reasonable to mix GAFF with OPLS force field in AMBER?
I have read though the mailing list and I found some people was mixing AMBER force field with the Glycam force field (e.g.
http://archive.ambermd.org/200906/0240.html). I knew that for GAFF, SCNB = 2.0 and SCEE = 1.2. What values are they in OPLS? Is it 1.0 since OPLS doesn't have any scaling? The combine rules of GAFF and OPLS for the Lennard-Jones potentials are different as well. GAFF follows the AMBER rules and OPLS uses geometric mean for sigma and epsilon. Is it possible to use two kinds of combine rules in AMBER?
Thank you for your help in advance.
Sincerely,
Guoxiong Su
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Received on Mon Feb 20 2012 - 14:00:02 PST
