AMBER Archive (2009)

Subject: [AMBER] MM_PBSA enquiries

From: s. Bill (s_bill36_at_yahoo.co.uk)
Date: Sun Nov 08 2009 - 08:53:04 CST

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

      
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