I may be off base here, but it doesn't seem like you are actually asking
about AMBER's constant pH simulations, but just making an input file from a
pdb.
If that is the case, then to my understanding LeAP will simply look at what
your residue is called in the PDB. If it is called GLU it will be the
negatively charged, non-protonated Glutamic acid. If it is called GLH it
will take it to be the protonated neutral form. So in that sense it does
not care about pH, it just takes what you give it in your PDB.
I can't seem to read your initial message though, so perhaps you are
actually talking about some kind of pH pKa prediction thing that LeAP can
perform.
On Thu, Feb 16, 2012 at 12:01 AM, <abinayar.imsc.res.in> wrote:
>
>
> Dear Mr.David Case,
>
> Thank you very much for that. But,then H++ server takes pH
> as an input parameter, what is the default value of pH
> that xleap would assume?
>
> Thanks in advance!
>
> With regards,
> Abinaya
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Aron Broom M.Sc
PhD Student
Department of Chemistry
University of Waterloo
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Received on Wed Feb 15 2012 - 21:30:02 PST
