On Wed, Apr 6, 2011 at 4:54 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Apr 05, 2011, Jason Swails wrote:
> >
> > Just a quick question -- does NAB have the variable 1-4 scaling added to
> > sander/pmemd?
>
> I'm pretty sure the answer is "no"; same question is now appropriate for
> mdgx
> as well....sigh
>
If I find some time to throw at this before anyone else gets to it, I'll try
to include that. My suspicion is that it will have to wait for amber12
(which is almost a certainty if I end up doing it). The reason I asked is
that it affects some of the fringe MMPBSA.py applications. Standard ones
will be unaffected, since internal potential terms cancel for
single-trajectory approaches, anyway. For multiple trajectories with
GLYCAM/Amber combos, though, users should probably be informed to use sander
(which MMPBSA.py currently allows you to force). I'll update the manual
when I figure out where I want to put it :).
Thanks!
Jason
>
> ...dac
>
>
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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 Wed Apr 06 2011 - 10:30:04 PDT
