Re: [AMBER] MMPBSA using counterions

From: Jason Swails <>
Date: Fri, 9 Jul 2010 10:44:04 -0400

You do not need a neutral receptor/ligand. You can add "ions" via saltcon
(or istrng for PB) to enhance the screening. The only ions you should
include are those that are critical for binding.

Hope this helps,

On Fri, Jul 9, 2010 at 3:08 AM, Giorgos Lamprinidis <> wrote:

> 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 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
> software.
> Dr. George Lamprinidis
> School of Pharmacy
> Univeristy of Athens
> Greece
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Jul 09 2010 - 08:00:03 PDT
Custom Search