On Tue, Oct 4, 2011 at 6:49 PM, Peter Eastman <peastman.stanford.edu> 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
corrections).
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).
HTH,
Jason
> Thanks!
>
> Peter
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Tue Oct 04 2011 - 16:30:02 PDT
