On Thu, Jun 14, 2012 at 5:10 PM, George Tzotzos <gtzotzos.me.com> wrote:
> Thank you all very much for the suggestions.
>
> To summarise, one can run
>
> 1. Constant pH in implicit solvent loading leaprc.constph
>
Correct (no ions here)
>
> 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.
>
Correct. Although changing GLU/ASP to GLH/ASH (and HIS to HIP) should be
done based on whether that residue is protonated or not according to
however you decide.
HTH,
Jason
>
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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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 Thu Jun 14 2012 - 15:00:03 PDT
