[AMBER] MMPBSA using counterions

From: Giorgos Lamprinidis <lamprinidis.pharm.uoa.gr>
Date: Fri, 9 Jul 2010 10:08:33 +0300

Dear AMBER users,

I have some questions regarding mmpbsa when the system has charge different
than 0.
I have a complex (receptor + ligand)
The receptor has charge -4 and the ligand +1. So i combine them and the
total charge is +3. I have to use the counterions command just before
solvate the complex or before?
If i neutralize the complex before solvating, at the end of the
calculations, when i use the mmpbsa.pl script the receptors file will have
charge -4 ,since they come from the .rec.prmtop file which is the original
before the use of counterions, and the complex file will have -3 (-4 +1 from
the ligand)
If i use counterions before i combine the receptor with the ligand the final
receptor file will have -1 and the ligand +1. However i am afraid if one
counter ion (Na+) is placed near a ASP residue which creates a salt bridge
with my ligand (which has protonated nitrogen)
So, please inform me about the best procedure to deal with systems, where
the ligand has charge, when i am using MMPBSA module.

Many thanks for you time and your marvellous job you are doing with AMBER

Dr. George Lamprinidis
School of Pharmacy
Univeristy of Athens

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Received on Fri Jul 09 2010 - 00:30:03 PDT
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