[gmx-users] Re: how many dihedral angles should be included for the naphthalene molecule if I use oplsaa

Alan alanwilter at gmail.com
Wed Apr 28 12:52:42 CEST 2010

I second Justin here, for Amber FF (which share essentially the same
topology but with different parameters with OPLS/AA), the impropers
dihedrals seems to be enough as for TRP.

Just a side note, using ACPYPE (which uses antechamber in the core) to
generate topologies for molecules like TRP, 6 extra impr. dihedrals are
added, but clearly not necessary.

You may want to try ACPYPE as I believe antechamber does a really good job
getting the topology (even if in excess of imp. dih as for TRP and probably
for napthalene), and of course check the literature as suggested by Justin.


On Wed, Apr 28, 2010 at 06:13, <gmx-users-request at gromacs.org> wrote:

> Ming Han wrote:
> >  1__2   6__
> > //     3\/     \\
> > |        ||4    |
> > \\___ /\___//
> >    5  7
> >
> >
> > I want to know if 1-2-3-6 torsion should be included?
> > And if both 2-3-4-7 and 6-3-4-5 should be included?
> > Thanks.
> >
> I would think that proper dihedrals would not even be used for such a
> molecule.
>  The fused ring systems will utilize impropers to stay planar.  For
> example,
> the TRP side chain specifies no proper dihedrals within the indole side
> chain;
> only impropers are used, but maybe someone with more OPLS derivation
> experience
> can comment.
> You can also look into the literature.  A simple Google search for
> "napthalene
> OPLS" (without the quotes) turns up tons of simulation papers.
> -Justin

Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
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