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 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
Tivani
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Received on Wed Oct 30 2013 - 02:30:03 PDT
