[gmx-users] Force Field => Residues PHE, TRP, TYR, HIS ?

[Tsjerk Wassenaar]

Hi Chih-Ying Lin,

There's no such thing as a pi bond in a classical force field, bonds
are merely connections with a certain distance based potential.

Gromacs doesn't deal with polarity, the distribution of charges, etc.
is part of the force field. Better check the papers relating to the
force field you're using. On the other hand, you might already be able
 to find the answers to your questions in the residue database for the
force field you're using...

Cheers,

Tsjerk

On Thu, Sep 2, 2010 at 6:41 PM, Chih-Ying Lin <chihying2008 at gmail.com> wrote:
>
> HI
>
> Residues PHE, TRP, TYR, and HIS are carrying "Rings", or say pi bonds.
>
> How does the Gromacs deal with polarity for all this four residues?
>
> Is a single charge assigned for each atom on the center of atoms of the four
> residues ?
>
> Is pi bond given for the four residues in the force field?
>
>
> Thank you
> Lin
>
>
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.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.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology /
University of Groningen
The Netherlands