AMBER Archive (2007)

Subject: Re: AMBER: Torsion Restraint on Glycosidic Bond

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Feb 16 2007 - 15:32:44 CST

please send the output file up to the first energy eval.

On 2/16/07, Seth Lilavivat <sethl_at_gatech.edu> wrote:
> Dear Amber Users,
>
> I am refining one of my models trying to hold a NA base in the syn
> conformation.
> I created an RST file and followed the protocol listed in the DNA tutorial.
> I
> applied my restraint to a NA structure that I had already minimized and then
> ran
> the annealing step. No matter what values I assign to the restraint, it
> doesn't
> seem to affect the particular base that much. It still ends up in the
> normal
> anti conformation. Am I going about this the right way?
>
> Thanks,
> Seth
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-- 
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Carlos L. Simmerling, Ph.D.
Associate Professor                 Phone: (631) 632-1336
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Stony Brook University        E-mail: carlos.simmerling_at_gmail.com
Stony Brook, NY 11794-5115
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