AMBER Archive (2003)

Subject: Re: AMBER: references about AMBER MD simulations

From: sd233_at_georgetown.edu
Date: Thu Aug 07 2003 - 10:04:39 CDT

Dear Dr.David A.Case:
Thank you very much for your reply and fruitful information.
Sincerely,
Sivanesan

D.Sivanesan, Ph.D.
Dept. of Oncology,
Lombardi Cancer Center,
Georgetown University, DC 20057

----- Original Message -----
From: "David A. Case" <case_at_scripps.edu>
Date: Wednesday, August 6, 2003 11:21 pm
Subject: Re: AMBER: references about AMBER MD simulations

> On Thu, Aug 07, 2003, sd233_at_georgetown.edu wrote:
> >
> > When I looked at the RMS plot (using carnal), after running 500PS
> of
> > MD simulations with WATERBOX (size 16A) for a protein, the RMSD
> lies
> > around 0.4Angstroms from the initial structure. Is it a healthy
> > simulation?
>
> Depends on what you really mean by "size 16 A": you could hardly
> fit a
> protein into a 16 Ang box if you want any reasonable distance between
> the protein and the edge of the box.
>
> An RMS shift (vs. what? an x-ray structure, a minimized structure?)
> of only
> 0.4 Ang. is unusually small. You may worry that fluctuations are
> beingunderestimated for some reason. But this is speculation since
> I know
> almost nothing about your simulation.
>
> >
> > Also Could anybody point out the references about AMBER MD
> simulations
> > for proteins with WaterBOX.
> >
>
> You should have no difficulty in finding hundreds of papers that
> describesuch simulations.
>
> ..good luck...dac
>
> --
>
> ==================================================================
> David A. Case | e-mail: case_at_scripps.edu
> Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
> The Scripps Research Institute | phone: +1-858-784-9768
> 10550 N. Torrey Pines Rd. | home page:
> La Jolla CA 92037 USA | http://www.scripps.edu/case
> ==================================================================
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