[AMBER] Free binding energy calculations for Zinc dependent ligands

From: Tivani Mashamba <tivanim.yahoo.co.uk>
Date: Wed, 30 Oct 2013 09:09:05 +0000 (GMT)

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 mmpbsa.in -o mmpbsa.dat -sp com_solvated.top -cp com.top -rp rec.top -lp LIG.top -y ZN1.top -lp ZN2.top -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.

I shall be very grateful if you can assist me on this.

Best wishes
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Received on Wed Oct 30 2013 - 02:30:03 PDT
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