[gmx-users] Simulation of protein at specific pH

Justin A. Lemkul jalemkul at vt.edu
Sun Apr 24 20:47:29 CEST 2011

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.


> Thanks
> Prerna


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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