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

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 2 19:01:19 CEST 2010

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...



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
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Tsjerk A. Wassenaar, Ph.D.

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

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