[gmx-users] energy of each residue??

Tsjerk Wassenaar tsjerkw at gmail.com
Tue May 1 13:57:01 CEST 2007

Hi Kota,

In your .mdp file, under energy_grps, you should list your residues.
As you didn't give much more information, it's hard to tell why grompp
bailed out. The error message is usually a good thing to add to a
mail, and in this case, the .mdp file might be too.



On 5/1/07, Pradeep Kota <kotanmd at gmail.com> wrote:
> Dear users,
> I'm trying to compute the contribution of each residue to the total energy
> of a protein. I neutralized my system with 8 chloride ions and then made an
> index file with each residue in a different index group, using 'splitres'
> via make_ndx. it gave me an index file with atoms of each residue in
> different index groups. but as all these atoms are again listed in the
> default index group - Protein, grompp shouts out a fatal error. there was a
> post on the list about index groups being bungled up after taking the system
> thro genion. but i dont think genion really matters in my case. any inputs?
> my idea is to calculate the energy of each residue in a given protein. i
> wish to run a simulation for 10 ps for that. am i going wrong anywhere? is
> there a better way?
> thanks in advance
> Kota.
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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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