Thank you all very much for the suggestions.
To summarise, one can run
1. Constant pH in implicit solvent loading leaprc.constph
2. "Constant protonation" loading leaprc.ff99SB renaming GLU and ASP to GLH and ASH, respectively, either in explicit or implicit solvent.
I take it that "constant protonation" is equivalent to standard MD.
Unless I hear from you otherwise, I shall assume that the above summary is correct
George
On Jun 14, 2012, at 10:55 PM, Jason Swails wrote:
> 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 - 14:30:03 PDT
