[gmx-users] Simulation of protein at specific pH
prernab2010 at gmail.com
Sun Apr 24 21:04:47 CEST 2011
Thank you so much Justin, that really helped :)
On Mon, Apr 25, 2011 at 12:17 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> prerna bhardwaj wrote:
>> Dear Gromacs User,
>> I want to simulate my protein at a specific pH. Using H++ server I have
>> generated my .pdb file at pH 5. But pdb2gmx is showing all the usual fatal
>> error "like "Atom HB3 in residue MET 1 not found in rtp entry with 17
>> atoms". But I can't use -ignh option, because it is bringing back at the
>> same normal stage. So what should I do I want to carry out simulation at pH
> It sounds like you should indeed be using -ignh because you have a
> malformed input. Under no conditions should the beta-carbon of methionine
> ever have three protons. Carbon atoms can't have five bonds. Either the
> atom naming in your .pdb file is wrong (which will cause pdb2gmx to fail) or
> the protonation state is wrong (which will cause pdb2gmx to fail in the
> absence of -ignh).
> You can set the protonation state of any titratable residues and termini
> using pdb2gmx -inter, in concert with -ignh, which appears to be necessary
> in your case.
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
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