Re: [AMBER] Using ff10 with ildn or nmr

From: Jason Swails <>
Date: Tue, 4 Oct 2011 19:18:35 -0400

On Tue, Oct 4, 2011 at 6:49 PM, Peter Eastman <> wrote:

> In the AmberTools manual (section 2.2.1), it says you can use the
> ff99SBildn and ff99SBnmr modifications along with ff10. It's rather vague
> on exactly how to do it, though, and my attempts so far have been
> unsuccessful. I hoped that if I just did "source leaprc.ff10" followed by
> "loadamberparams frcmod.ff99SBildn" that would have the right effect, but it
> didn't: the resulting prmtop was identical to what I get with ff10 alone.
> And I don't see how this could ever work. ff10 uses different atom types
> from either ff99 or ff99SBildn, so those files just can't be used together.
> What am I missing? What is the correct way to combine those modfication
> sets with ff10?

For proteins, ff99SB == ff10 (I've verified this with several proteins. The
topology files are different, but the simulation results are spot on). For
anything besides proteins, ff99SB == ff99SBildn == ff99 (bsc0 is the proper
force field to use for nucleics, or ff10 which is ff99bsc0 + other torsion

Moreover, I believe that ff99SBildn is, itself, ff99SB + DESRES
modifications, so what you're looking for *should* be just sourcing
leaprc.ff99SBildn. If you want to treat mixed nucleic-protein systems, I
would suggest performing surgery on the relevant leaprc files to create your
own leaprc (copy the nucleic acid imports from ff10 while you take the
protein parts from ff99SBildn).


> Thanks!
> Peter
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
AMBER mailing list
Received on Tue Oct 04 2011 - 16:30:02 PDT
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