Re: [AMBER] Fitting Torsional parameters

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Mon, 15 Feb 2010 11:07:05 -0500 (EST)

What exactly do you mean with 'the function is only fit to a single
fourier term' ? The E_tors can have as many cosine terms in it as
possible. For instance, in the parm99.dat file, you have the following
torsion defined:

CT-CT-CT-CT 1 0.18 0.0 -3.
CT-CT-CT-CT 1 0.25 180.0 -2.
CT-CT-CT-CT 1 0.20 180.0 1.

This parameter set is to define the torsion energy of CT-CT-CT-CT with
different PHASE, PK, and PN values (IDIVF is equal to 1) which will have 3
cosine term to define the CT-CT-CT-CT torsional energy. You can increase
the level of accuracy by increasing the number of cosine terms used to
define a particular torsion.

   Ilyas Yildirim, Ph.D.
   ---------------------------------------------------------------
   = Hutchison Hall B#10 - Department of Chemistry =
   = - University of Rochester =
   = 585-275-6766 (office) - =
   = http://www.pas.rochester.edu/~yildirim/ =
   ---------------------------------------------------------------

On Mon, 15 Feb 2010, stephane acoca wrote:

> Hi, I would like to clarify the protocol for adjusting torsional
> parameters. The problem I am having is that after fitting to a fourier
> series the energy difference between the QM and MM energies (torsion
> not included in MM Energy), the frcmod specifications I find point to
> :
>
> IDIVF
> PK
> PHASE
> PN
>
> Meaning that the function is only fit to a single fourier term of the format :
>
> Etors = (PK/IDIVF)*(1+ COS(PN*PHI - PHASE)
>
> Aren't higher level fourier terms available to be specified torsion
> parameters. I couldn't find the information in either Amber manual
> 8,9, or 10. Any guidance would be appreciated.
>
> Stephane Acoca
> McGill University
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>

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Received on Mon Feb 15 2010 - 08:30:03 PST
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