[gmx-users] ionomer topolgy

Justin Lemkul jalemkul at vt.edu
Tue Oct 1 22:45:41 CEST 2013

On 10/1/13 1:03 PM, Ehsan Sadeghi wrote:
> Hello,
> When I use pdb2gmx, the bonds between atoms in the generated conf.gro or conf. pdb file are misplaced. I am using Avogadro for building the atomistic structure, it uses "connect" command to connect atom correctly. After running pdb2gmx, the generated files do not have "connect" and they put the bonds is some random places. An suggestion for solving this problem or any other software for building structure without having this problem?

The only bonds assigned are what you specify in the .rtp file.  If it's not 
right, fix the .rtp.

> If I just want to consider bond stretching in my analysis, what should I do to tell gromacs neglect angle,improper, and dihedral? I received 89 errors for not defining them.

You'd remove them from the topology entirely.  That will be a seriously flawed 
physical model, unlikely to produce any useful results.



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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