[gmx-users] Impact of ignoring hydrogens

Repic Matej matej.repic at epfl.ch
Mon Aug 31 15:04:30 CEST 2015

Dear Suniba,

The -ignh flag of pdm2gmx removes all the hydrogens from the pdb file and
then adds them according to simple geometric rules. This should be fine
for most hydrogens except for the exchangable protons of acidic and basic
residues, where the algorithm quite possibly will not protonate all
residues the same as in the NMR structure. Strictly, it is not necessary
to remove the experimental data to make the simulation run, but it does
make it more tedious.

The problems with pdb2gmx arise because the naming of H atoms in
forcefield rtp/hbd files is not the same as in the pdb, thus you get quite
a lot of errors. The solution is rather straighforward -> rename the
hydrogens in your pdb to they match those from
$GMXDATA/top/ffname/aminoacids.rtp. How you go about renaming efficiently
is an entirely different thing.


Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
BCH 4108
CH - 1015 Lausanne


On 8/31/15, 14:15, "gromacs.org_gmx-users-bounces at maillist.sys.kth.se on
behalf of su" <gromacs.org_gmx-users-bounces at maillist.sys.kth.se on behalf
of sun.iba2 at gmail.com> wrote:

>Hello All
>I am doing protein ligand MD to view the interactions and effect of
>ligand on protein structure. However the NMR structure of protein
>encountered some warnings and considering that, i ignored hydrogens by
>-ignh. I believe that the hydrogen bonding might reduce due to this
>action. Is that true? Can anyone please clear me what happens after the
>application of -ignh.
>Thank You
>Sent from my iPhone
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