AMBER Archive (2003)

Subject: question about MM-PBSA?

From: Lishan Yao (yaolisha_at_pilot.msu.edu)
Date: Tue Apr 08 2003 - 12:21:20 CDT

Hi there:
   I run 500ps MD for my ligand in water. Now, I try to use MM-PBSA to
decompose the energy. Actually I'm only interested in the interaction between
ligand and the solvent. This is what I did:
DCTYPE 3
#
COMREC 2-1218
COMLIG 1-1
COMPRI 1-1218
RECRES 1-1217
RECPRI 2-1218
RECMAP 1-1217
LIGRES 1-1
LIGPRI 1-1
LIGMAP 1-1

I have one ligand and 1217 wat molecules. The only thing I want to get is the
total interaction energy between this ligand and all the water molecules. So is
this the right way to do it? Should I change some parameters?
 Thanks!

Sincerely
Lishan