Re: [AMBER] Free binding energy calculations for Zinc dependent ligands

From: Jason Swails <>
Date: Wed, 30 Oct 2013 08:52:10 -0400

On Wed, Oct 30, 2013 at 5:09 AM, Tivani Mashamba <>wrote:

> Hi
> I am trying to calculate binding free energy for Zinc dependent receptor:
> ligand system, my receptor containd 2 Zinc atoms and the ligands are Zn
> depedent. I have included the 2 Zn atoms in the SUB, see below:
> pirun -np $nproc -machinefile $PBS_NODEFILE $exe -O -i -o
> mmpbsa.dat -sp -cp -rp -lp -y
> -lp -y md.mdcrd > mmpbsa.log
> However, I am not getting any result and here is the error message that I
> am getting.
> PrmtopError: Complex natom != receptor natom + ligand natom
> Exiting. All files have been retained.

Your topology files are incompatible. One of the properties that
checks is that there are as many atoms in the bound state (complex natom)
as there are in the unbound state (receptor natom + ligand natom). Your
topology files fail this test. You need to find out why your atom numbers
do not match between your complex and receptor/ligand topology files and
fix it.

Good luck,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Wed Oct 30 2013 - 06:00:03 PDT
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