On 2011-04-24 20.47, Justin A. Lemkul 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.
It doesn't have three protons but the official (IUPAC/IUPAB) side chain
atom naming is: CG (counts as 1) HB2 HB3, so the H++ server is correct,
and the braindead force fields are wrong.
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
--
David van der Spoel, Ph.D., Professor of Biology
Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone: +46184714205.
[email protected] http://folding.bmc.uu.se
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