Re: [AMBER] Puzzles about calculating binding energy using MMGBSA

From: Jason Swails <>
Date: Sat, 14 Dec 2013 09:44:07 -0500

On Sat, Dec 14, 2013 at 7:05 AM, Yanyan ZHU <> wrote:

> Hi all:
> I am a graduate student in Sichuan university from China. I have some
> puzzles as following: I want to calcuate the binding energy of residues
> after calculating the integral binding energy of complex successfully. In
> my input files,x-wat-com.prmtop, x-wat-pro.prmtop ,x-wat-lig.prmtop are the
> prmtop of complex ,receptor and ligand respectively. And in my system , the
> number of atom for complex, receptor and ligand are 4521, 4484 and 37
> respectively. The dielectric constant of the composite solvent in my system
> is 56.97.
> My problem is that I can successfully calculate the binding energy
> through the input file of and However, I can not
> achieve the calcuation of residues through the input file of and
> I am looking for you replay and will be very grateful for your
> kindhearted.

Can you accomplish what you want to do using instead?
typically receives a little more support on the mailing list.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Sat Dec 14 2013 - 07:00:03 PST
Custom Search