[gmx-users] Impact of ignoring hydrogens
peter.stern at weizmann.ac.il
Mon Aug 31 16:52:26 CEST 2015
Matej is correct, but doing that can be quite tiresome. Easier I believe to just map the unrecognized names in the arn file ($GMXDATA/top/ffname/aminoacids.arn
Atom renaming database
Force fields often use atom names that do not follow IUPAC or PDB convention. The .arn
database is used to translate the atom names in the coordinate file to the force field names. Atoms
that are not listed keep their names. The file has three columns: the building block name, the old
atom name, and the new atom name, respectively.
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Repic Matej
Sent: Monday, August 31, 2015 4:04 PM
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Impact of ignoring hydrogens
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 SB - ISIC LCBC 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:
>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.
>Sent from my iPhone
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