On Thu, Jun 14, 2012 at 4:23 PM, David A Case <case.biomaps.rutgers.edu>wrote:
More disturbing, however, is the fact that you are loading leaprc.constph
> for
> a solvated simulation. Unless I am missing something( Jason???) Amber12
> does
> *not* support constant pH in explicit solvent.
Correct. Amber 12 does NOT have constant pH in explicit solvent. Amber
13(?) should. If you are running constant pH MD, you are doing so in
implicit solvent (or you get an error message).
You can use CpHMD in IMPLICIT solvent to determine protonation states, then
run constant protonation MD with those states in explicit solvent. Or, you
can use H++/PROPKA to determine those protonation states for your constant
protonation MD in explicit solvent.
All the best,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jun 14 2012 - 14:00:04 PDT
