AMBER Archive (2009)

Subject: [AMBER] ligand parameterization

From: Nahoum Anthony (
Date: Thu Nov 26 2009 - 04:49:51 CST

Dear Amber users,

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 ?

Thanks for your time,


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