[gmx-users] changing pdb file residue name

Tsjerk Wassenaar tsjerkw at gmail.com
Mon Jul 6 08:36:35 CEST 2009

Hi Rukmani Sridharan,

It's not a matter of name. Gromacs is unlikely to have a topological
description of the molecule and you have to provide that. See




On Mon, Jul 6, 2009 at 6:06 AM, Rukmani
Sridharan<rukmani.gromacs at gmail.com> wrote:
> Hi,
> I am a bit new to gromacs and am familiarizing myself with the various
> commands. I want to simulate an unusual molecule, with the formula C7H10.
> The downloaded pdb file had the residue mname MON which gromacs does not
> recognize. How should i name the residue?
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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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