Re: AMBER: references about AMBER MD simulations

From: David A. Case <>
Date: Wed, 6 Aug 2003 23:21:05 -0700

On Thu, Aug 07, 2003, 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 being
underestimated 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 describe
such simulations.

...good luck...dac

David A. Case                     |  e-mail:
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            |
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Received on Thu Aug 07 2003 - 07:53:01 PDT
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