questions about AMBER_SERVER

From: Sylvie Derreumaux <>
Date: Tue 08 Feb 2000 17:21:38 -0800

Dear AMBER authors,

I would like to submit a pdb file to the AMBER_SERVER for an energy
calculation. It consists of the averaged DNA structure of a MD
simulation performed with AMBER and parm98.
I have some questions:

Does the short in vacuo minimization performed by the AMBER_SERVER is
sufficient to relax an averaged MD structure?

Is the minimization performed without counterions? If not, does it use
the IB solvated sodium model, and how are they placed around the DNA?

Is it possible to perform the minimization and the MM energy calculation

with the parm98 force field (instead of parm94)?

Thank you very much for your help.

Sylvie Derreumaux

Departement de Biolobie et Pharmacologie Structurales
Institut Gustave Roussy
Received on Tue Feb 08 2000 - 17:21:38 PST
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