Re: [AMBER] Comparing dihedral energy curves

From: Ilyas Yildirim <yildirim.pas.rochester.edu>
Date: Mon, 26 Apr 2010 13:15:53 -0400 (EDT)

Lekpa,

Take a look at the following article:

"Reparameterization of RNA Torsion Parameters for the AMBER Force Field
and Comparison to NMR Spectra for Cytidine and Uridine", Ilyas Yildirim,
Harry A. Stern, Scott D. Kennedy, Jason D. Tubbs and Douglas H. Turner
http://pubs.acs.org/doi/abs/10.1021/ct900604a

We reparameterized the CHI torsions for the RNA residues. What you want to
do is probably similar to what we did. Hope this helps.

Best,

   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, 26 Apr 2010, Lekpa Duukori wrote:

> Hi all,
>
> I want to compare (QM vs MM) dihedral energy curves for a carbohydrate
> (glycam) link to amber parameters but I am not entirely sure how to proceed.
>
> During the QM calculations do I remove all other rotations around this bond,
> eg * OS CG * R (OS and CG being the linking bond in this case) in the say
> Gaussian input file?
> Same question about MM calculation. Also for MM do I divide the energy
> differences (Vn) by the number of rotations about that bond before comparing
> ? I guess this should depend on if other rotations are removed.
>
> Thanks for your time.
>
> Lekpa
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
>

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Received on Mon Apr 26 2010 - 10:30:03 PDT
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