AMBER Archive (2003)

Subject: Re: AMBER: double bonds in prmtop

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Fri Sep 19 2003 - 15:24:18 CDT

Hi,

I do not think that information is contained in the PDB file but that's
why you generate the topology. You read the atom names and AA sequence
from the PDB file and you know which atom is sp2 or sp3 and you associate
the right atom type from the force field. The force field then defines
what constants to use in the potential depending on the atoms involved in
the same bond, angle, torsion etc.

In the pdb file you have the atoms coordinates but the "equilibrium" bonds
in the simulation are those defined by the FF.

I assume that's how this works.

Ioana

On Fri, 19 Sep 2003, Herbert Georg wrote:

> I would like to know how does AMBER treat double bonds. How does it know
> if a bond is a single or doube or even a triple one? Does it use the
> bond lenght given, by PDB file for example, as R0 or it uses the lenght
> given by literature?
>
>
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