Thank you so much Justin, that really helped :) On Mon, Apr 25, 2011 at 12:17 AM, Justin A. Lemkul <[email protected]> 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 > > ======================================== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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