Dear Guoxiong Su,
Mixing two force fields is always dangerous.
I would compute a highly consistent set of charges for all the
molecules to be studied. If you want to use OPLS you can find a RESP
approach for OPLS.
See R. H. Henchman and J. W. Essex, J. Comput. Chem., 1999, 20, 483?498.
This approach should be easy to implement in the R.E.D. program.
A new box for benzonitrile can be created for Amber.... Then, whatever
you decide to use (may be try first SCNB = 2.0 & SCEE = 1.2) your
benzonitrile box has to be tested/studied...
regards, Francois
> 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?
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Received on Tue Feb 21 2012 - 08:30:02 PST
