Hello Amber Users,
I want to calculate binding free energy of a complex having five identical
ligands. I really do not know how to define the ligand prmtop file in
MMPBSA.py.
I tried something like
mpirun -np 8 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmgbsa-1.in -o
SAA_2_hexa_104_S1_mmgbsa.dat -do SAA_2_hexa_104_S1_mmgbsa-decomp.dat -cp
com.prmtop -rp rec.prmtop -lp lig1.prmtop lig2.prmtop lig3.prmtop
lig4.prmtop lig5.prmtop -y SAA_2_hexa_104_S1.crd
However, it is not working. Can anyone please suggest me how to use
multiple ligands in a single MMPBSA calculation? Any suggestion would be
appreciated.
Thanks,
Prabir
--
*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*
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Received on Fri Mar 29 2019 - 14:30:03 PDT
