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-- Jason M. Swails Quantum Theory Project, University of Florida Ph.D. Candidate 352-392-4032 On Feb 16, 2012, at 12:22 AM, Aron Broom <broomsday.gmail.com> wrote: > 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 >> >> >> _______________________________________________ >> AMBER mailing list >> AMBER.ambermd.org >> http://lists.ambermd.org/mailman/listinfo/amber >> > > > > -- > Aron Broom M.Sc > PhD Student > Department of Chemistry > University of Waterloo > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Fri Feb 17 2012 - 05:00:03 PST