On Tue, Jun 2, 2015 at 4:28 AM, Jeffrey Teillet <jteillet.laas.fr> wrote:
> Hello,
>
> I'm a french student who's studying de parametrization of the
> ambertools14 software for the purpose of a work experience.
> I'm mailing you since you could help me understand some points.
>
>
> I don't understand those torsions :
>
> /X -CT -N2 -X 6 0.00 0.0// JCC,7,(1986),230/
>
> There are a lot of torsions with no energy. Is the torsion exist ? How
> to take those torsions in consideration with no energy ? Maybe there's
> something important i can't notice.
>
Torsion profiles are made up of both nonbonded terms (the van der Waals
and electrostatic interactions between atoms separated by 3 bonds are
typically scaled by some constant). In some cases, it's certainly possible
that these electrostatic and van der Waals interactions is enough to
reproduce the correct torsion profile. In that case, no extra correction
is needed from the torsion potential in order to reproduce the correct
torsion profile.
However, the dihedrals still need to be in the topology file, because
that's how sander and pmemd know that two atoms are separated by 3 bonds
(and therefore need their nonbonded interactions scaled).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jun 02 2015 - 08:30:02 PDT
