[gmx-users] Fw: Gromacs error regarding default gromos bond type and angle type

Negar Parvizi negar.parvizi at yahoo.com
Mon Dec 29 21:00:34 CET 2014

Dear Gromacs users

we want to simulate 1EA1 pdf file using gromacs. (according to justin tutorial).

This pdf file contains two cofactors including TPF and HEM. Our next step is to dock some antifungal drugs to this protein which is cytochrome of the fungi.
As the TPF was not located in the active site and due to the lack of topology informtaion for this cofactor in gromos force fields, we omitted the TPF .
Then we performed pdb2gmx on the protein along with the HEM cofactor. The pdb2gmx did not give error, so we were satisfied with the topology file.

But when in the step of adding ions, we performed grommp command to get the ions.tpr file, we faced with 7 errors:

these errors were saying that there are not gromos default bond type or angle type or dihedral type for specified lines in the topology file.

I checked the atom numbers that were present in those bonds, angles and dihedrals and came to the conclusion hat all of them contain (Fe) atom which is present in the HEM cofactor.

It seems that pdb2gmx command is not able to specify gromos default bond type or angle type whenever Fe is there.

Now please guide us to solve the problem.
what should I put in the vacancy spaces for these bond type or angle types. I mean what (gb_? or ga_?)
and why the pdb2gmx did not gave error???

Thanks alot

Dr. Delara Mohammad-Aghaie
Assistant Professor of Physical Chemistry
Department of Chemistry
Shiraz University of Technology



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