Re: [AMBER] Comparing dihedral energy curves

From: Lekpa Duukori <duukori.gmail.com>
Date: Mon, 26 Apr 2010 12:56:50 -0600

Thanks Ilyas. This provides some clarity.

Lekpa

2010/4/26 Ilyas Yildirim <yildirim.pas.rochester.edu>

> 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/<http://www.pas.rochester.edu/%7Eyildirim/> =
> ---------------------------------------------------------------
>
>
> 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
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>>
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Received on Mon Apr 26 2010 - 12:00:04 PDT
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