Re: [AMBER] periodic boundary condition

From: Jason Swails <>
Date: Thu, 15 Apr 2010 07:02:39 -0400


Take a look at the imin=5 option in sander (manual). That will let
you process a trajectory just as though it were a series of input
coordinate files. Choosing a maxcyc of 0 or 1 will simply extract the
energies. I believe you are able to set ntb=1 or 2 (equivalent in the
case of a single-point energy calculation I believe). You can then
proceed to use ptraj to strip the ligand from the receptor and analyze
the receptor alone with this method and the same for the ligand
(you'll need separate, compatible prmtops for each step). Then taking
the difference complex - receptor - ligand will give you the binding
energy. This is basically MM/PBSA with periodic boundary

Good luck!

On Thu, Apr 15, 2010 at 1:11 AM, juan zeng <> wrote:
> Dear amber users:
>          I want to calculate the binding affinity on protein-ligand complex
> with the linear interaction energy method,in this environment the binding
> affinity comprises Van der waals interaction potential and electrocstatic
> interaction potential.while others used the non-periodic boundary condition
> to calculate the binding affinity before,now I wish that this calculation
> can be done in the periodic boundary condition.but the molecules in cell far
> away from the center cell will interaction with the protein-ligand complex
> in the center cell,so I need to find out a method that can calculate the
> interaction energy(especially the electrostatic interaction energy) of the
> complex with all other molecules in the whole simulation system.Can you give
> me some suggestion how to make this calculation be realized.
>        Hope receive your reply.
> Juanzeng
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Thu Apr 15 2010 - 04:30:03 PDT
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