[gmx-users] Simulation of protein at specific pH

[prerna bhardwaj]

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
>> 5.
>>
>>
> 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
>
>  Thanks
>> Prerna
>>
>>
> --
> ========================================
>
> 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
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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