AMBER Archive (2009)

Subject: Re: [AMBER] ligand parameterization

From: case (
Date: Thu Nov 26 2009 - 09:09:05 CST

On Thu, Nov 26, 2009, Nahoum Anthony wrote:
> I want to parameterize a ligand for which the default torsion term given
> in the .frcmod file by antechamber is inadequate. I've used Gaussian to
> do a torsion scan and get an energy plot for the full rotation and I
> want to fit that energy plot using Amber's force field equation. I've
> read several papers where people have done this sort of things, but I
> can never quite get if they fit the Gaussian energy with the full force
> field equation, allowing only the torsional parameters to vary or if
> they try to fit only the torsional part of the force field equation to
> the Gaussian results. What is the correct procedure, if any ?

The former: you need to compare the total energy from Gaussian to the total
energy from the force field.

...good luck...dac

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