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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