Re: [AMBER-Developers] [AMBER] manual prmtop file editing for free energy calculation

From: Jason Swails <>
Date: Tue, 29 May 2012 11:49:10 -0700

On Tue, May 29, 2012 at 4:54 AM, David A Case <>wrote:

> On Mon, May 28, 2012, Ross Walker wrote:
> >
> > Out of interest how does Leap know to use different combining rules for
> > OPLS?
> The "AC" vs. "RE" flag in the non-bonded section triggers a change in
> combining rules. (I think! check the code or run a simple test
> calculation.)

This isn't going to help my case, but I don't see where this happens.
 mathop.c, line 69 (function MathOpConvertNonBondToAC). This only appears
to satisfy the Amber combining rules. That function itself is only called
in two places in unitio.c (and nowhere does it look like we try to match
"RE" or "AC"). So unless I'm missing something, OPLS just gets the Amber
combining rules inside tleap...

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER-Developers mailing list
Received on Tue May 29 2012 - 12:00:03 PDT
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