On Tue, Oct 04, 2011, 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.
Although ff10 for proteins is functionally the same as ff99SB, the
innards are quite different, since some new atom types have been added
(in preparation for ff11....) So, if you want to use ildn + SBnmr, try
staying away from ff10. I'd start with leaprc.ff99SBildn, and see if
adding the frcmod.ff99SBnmr to that works. Of course, make a simple
peptide and see what you get (rdparm can format the results to help out.)
I've not done this myself, but you (Peter) should be as good as anyone by
now at cobbling things like this together.
(It may be harder than one thinks, since ildn itself may be defining new atom
types that frcmod.ff99SBnmr won't know about. You might ask the DESRES people
if they have any experience along these lines.)
...dac
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Received on Tue Oct 04 2011 - 17:00:02 PDT
