Dear AMBER
I am going to do MM-PBSA calculation, in this caluclation I need to creat prmtop files for protein, ligand and protein-ligand.
I was wondering about my protein, my protein PDB file has some crystallic water molecules, should I delete these water molecules when I creat my protein prmtop file in gas phase?
Also, in tutorial no A3, you defined the following values:
SURFTEN 0.0072
SURFOFF 0.00
from where did you get these values? according to the manual these values should be:
SURFTEN 0.00542
SURFOFF 0.92
are they equal in the meaning, or what?
Thanks in advance;
Sincerely;
S. Bill
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Nov 08 2009 - 07:00:03 PST
