[gmx-users] pdb2gmx and his-heme group

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Jan 18 08:32:14 CET 2007

Hi Anthony,

Are the bonds and angles themselves listed? They should be, with no
further parameters (bond/angle type) specified. Running grompp should
then give you some warnings about missing parameters and "using
defaults". These defaults are given in ff*bon.itp, listed at the end
of the file. They are given for combinations of atoms, such as N - FE
in the case of heme. You could try to dump the .tpr file with gmxdump
and look for the bonds/angles to see if they are indeed listed
correctly. However, although I'm not completely sure, I think they
should be given with the option -pp, in which case there may indeed be
something wrong.

Hope it helps,


On 1/18/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> Anthony Cruz Balberdi wrote:
> > Hi user:
> >
> > Today I have been working with a heme protein and I notice that in the topology the parameters that include the His
> > (NE2) and the heme (FE) were not present in the topology (bon type, angle type, etc). Also when I check the topology
> > after grompp (-pp) this file also do not include the parameters. This is normal?? I am using gromacs 3.2.1 .
> Were they present as residues in the .rtf file? Did you read the
> warnings from pdb2gmx and/or grompp about things being missing?
> Mark
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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