AMBER Archive (2009)

Subject: RE: [AMBER] ligand parameterization

From: Nahoum Anthony (nahoum.anthony_at_strath.ac.uk)
Date: Thu Nov 26 2009 - 11:19:47 CST

Thanks for your help Dave and Jason, but your latest reply confuses me a bit...
The force field equation as given p.19 of the Amber 10 manual shows terms for bonds, angles, dihedrals, vdW (12-6 L-J), dielectric and polarization (if explicitly desired for the latter). I'd always considered the dihedral term to represent the torsional energy, so where is the 1-4 interaction term ? is it just part of the vdW and dielectric ?

Thanks again for your time,

Nahoum

________________________________________
From: amber-bounces_at_ambermd.org [amber-bounces_at_ambermd.org] On Behalf Of Jason Swails [jason.swails_at_gmail.com]
Sent: 26 November 2009 15:47
To: AMBER Mailing List
Subject: Re: [AMBER] ligand parameterization

Don't forget to zero out the torsional term in the force field. The 1-4
interactions will account for some of the profile, so the torsion term is
just a correction for the 1-4 inadequacies. Then you can do the same scan
with amber as you did with Gaussian and fit the difference to the fourier
terms that define the torsion.

Good luck!
Jason

On Thu, Nov 26, 2009 at 10:09 AM, case <case_at_biomaps.rutgers.edu> wrote:

> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber

_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber