[gmx-users] Calculating energies of amino acids in a protein using g_energy

Tsjerk Wassenaar tsjerkw at gmail.com
Wed May 16 06:39:10 CEST 2007

Hi Abhiga,

If I were you, I'd first focus on getting the simulation running. As
Anton mentioned in the mail you refer to, you can calculate the
energies for specific groups after doing the simulation (i.e.
performing a 'rerun').
Anyway, your problem is completely unrelated to the interaction
energies of your residues. Browse the archives for a solution (search
for topol.top not match out.gro, or something along these lines).



On 5/16/07, Mark Abraham <Mark.Abraham at anu.edu.au> wrote:
> abhigna polavarapu wrote:
> > Hi,
> >      I have to calculate the energy of each amino acid in the protein.
> > In one of the questions in mailing list
> > http://www.gromacs.org/pipermail/gmx-users/2001-November/000222.html
> > <http://www.gromacs.org/pipermail/gmx-users/2001-November/000222.html>
> > I came across this and this is what exactly what i should do. Can you
> > please explain that in a more clear way as I am getting an error when i
> > editted the steep.mdp file for the energygrps option saying that the
> > topology file topol.top does not match the out.gro file.
> Does your problem also happen when you don't edit the .mdp file?
> 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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