Re: [AMBER] new force field ff99SBildn not supported for normal mode analysis in amber11

From: Jason Swails <>
Date: Mon, 14 Feb 2011 15:20:22 -0500


I was just working on a response when Professor Case's came in, which
correctly identifies the problem

On Mon, Feb 14, 2011 at 2:54 PM, case <> wrote:

> On Mon, Feb 14, 2011, Tan Yaw Sing wrote:
> >
> > I created prmtop files using the new ff99SBildn force field and used them
> as
> > input for and The calculation stalls for
> > and gives an error that says that nmode is not working properly for
> > I looked through the output files and found a line that
> said
> This is because the ILDN force field introduced (for the first time in
> "Amber"
> history) a 5-fold torsional term.
> We are working on a fix. Jason: can you check the changes in commit
> 7be394c7a7 ? This applies a fix (I hope!) to what you did in sff2.c, and
> then
> adds the some functionality to eff.c (in sff) and ephi.f (in nmode).
> Please
> double-check my math...thanks....dave

I looked over your last patch; I did make a mistake copying over the first
derivative of the term that you properly fixed, and the rest looks good. If
you haven't already checked it, I am quite confident that the expression for
cos^5 is correct as implemented (though obviously that made the 1st
derivative term incorrect). Assuming those terms aren't needed in any other
places, that should fix the issue.

All the best,

> ....dac
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Mon Feb 14 2011 - 12:30:04 PST
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