[gmx-users] energy of each residue??

[Tsjerk Wassenaar]

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.

Cheers,

Tsjerk

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.
>
> _______________________________________________
> gmx-users mailing list    gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read
> http://www.gromacs.org/mailing_lists/users.php
>


-- 
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