Solvated protein...

From: Antonello Romani <>
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
 Tel : +39 0521 903 764
 Fax : +39 0521 903 742
 E-Mail :
Received on Mon Oct 25 1999 - 05:06:24 PDT
Custom Search