AMBER Archive (2009)

Subject: Re: [AMBER] ligand parameterization

From: Jason Swails (jason.swails_at_gmail.com)
Date: Thu Nov 26 2009 - 16:12:34 CST

Hello,

The 1-4 interaction term is a scaled non-bonded term. It has the same
functional form as the regular non-bonded interactions (VDW and EEL), but it
is simply scaled down. They are unique to atoms 3 bonds separated from one
another. Thus, this term will influence your dihedral profile, so you need
to account for it when you create your dihedral parameters (i.e. you do not
want to include the 1-4 effects in your dihedral fourier expansion, since
they will then be doubly-counted in your force field).

Note that the torsional term does NOT represent the torsional energy. In
the amber force field, it is nothing more than a correction to account for
effects that are not represented by the classical 1-4 interactions. A good
example is the minimum energy angle between biphenyl (C12H10). VDW and EEL
terms would favor a 90 degree angle between the planes of the two benzene
rings. However, this state is quantum mechanically unfavored because it
breaks all delocalization between the two pi systems of the benzene rings.
Thus, the 1-4 interactions correctly place a maximum energy at a 0 degree
separation (i.e. completely planar), but fail to put a local maximum at 90
degrees. This effect must be accounted for by the torsional term, but you
don't want to add the disfavoring of the completely planar angle, since that
is already accounted for by the 1-4 terms.

I hope this helps,
Jason

On Thu, Nov 26, 2009 at 12:19 PM, Nahoum Anthony <
nahoum.anthony_at_strath.ac.uk> wrote:

> 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
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>
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> 

-- 
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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