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
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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
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Received on Mon Oct 25 1999 - 05:06:24 PDT
