[gmx-users] editbox removes dummy atoms

Justin A. Lemkul jalemkul at vt.edu
Thu Jun 28 16:44:32 CEST 2012

On 6/28/12 10:40 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
> I have found out that there was always the same residue number for all the
> dummy atoms. Perhaps that was the failure. Now I changed it so that they
> have all different residue numbers. But now I get the error:
> Atom N is used in an interaction of type improper in the topology
> database, but an atom of that name was not found in residue
> number 309.

What is residue 309?

> when I want to put hydrogens to the structure.
> pdb2gmx -f 3m71_mod.pdb -o 3m71.gro -p 3m71.top -water tip3p -ff amber03 2>>l
> ogErr 1>>logOut

In my opinion, it is a far better approach to run only known macromolecules 
(proteins and DNA) through pdb2gmx, and add anything else afterwards and 
#include appropriate topologies.  Dealing with complex, heterogeneous systems 
may not always work, especially in the case where you've got dummy atoms that 
pdb2gmx won't recognize, unless you've done the leg work to incorporate them 
into your force field properly.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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