AMBER Archive (2000)

Subject: questions about AMBER_SERVER

From: Sylvie Derreumaux (derreuma_at_igr.fr)
Date: Tue Feb 08 2000 - 19:21:38 CST

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
CNRS UMR 8532
Institut Gustave Roussy
Villejuif
France