Solvated protein...

From: Antonello Romani <A.Romani_at_leonardo.biomed.unipr.it>
Date: Mon 25 Oct 1999 13:06:24 +0100

Dear Amber users,

I have to check the stability of my protein structure. So before to start md run
I have solvated my protein, already minimized, with SolvateBox command of XLeap.
The box dimensions are 52 x 67 x 56 A with solute and 3000 water molecules.
To relieve the initial steric clashes I have done a "steepest descent" minimization
during which only solvent molecules are allowed to move.

At the end of minimization the van der Waals energy was extremely higher than starting.

I have test several combination of parameter with the same results?

Is there someone that helps me ???


Best regards

Antonello Romani

 ___________________________________________
 Antonello Romani
 Istituto di Patologia Generale
 Plesso Biotecnologico Integrato
 Facolta' di Medicina e Chirurgia
 Universita' degli Studi di Parma
 via Volturno 39
 43100 Parma
=20
 Tel : +39 0521 903 764
 Fax : +39 0521 903 742
 E-Mail : A.Romani_at_leonardo.biomed.unipr.it
 ___________________________________________
Received on Mon Oct 25 1999 - 05:06:24 PDT
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