Ptraj can calculate some hydrogen bonding populations and such. Take a look
at its description in the AmberTools manual.
Good luck!
Jason
On Sun, Dec 5, 2010 at 3:56 AM, leila karami <karami.leila1.gmail.com>wrote:
> Dear amber users
>
> I did simulation of protein-dna complex in explicit waters by gromacs.
>
> and now I want to study hydrogen bond : direct and indirect (water
> mediated). Can I use amber for that? is it true?
>
> if so, what input files are necessary for hydrogen bond analysis by amber?
> How to convert gromacs file to amber files?
>
> any help will highly appreciated
>
> --
>
> Leila Karami
> Ph.D. student of Physical Chemistry
> K.N. Toosi University of Technology
> Theoretical Physical Chemistry Group
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Dec 05 2010 - 11:30:05 PST
