Dear Amber Users:
I want to calculate binding free energy for a complex with two small
molecule ligands using three trajectories. I set receptor+lig1.nc for the
receptor trajectory, and lig2.nc for the ligand trajectory. The detailed
command is as follows:
mpirun -n 8 $AMBERHOME/bin/MMPBSA.py.MPI -O -i mmpbsa.in -o reclig1_lig2.dat
-sp complex_water.prmtop -cp rec_lig1_lig2.prmtop -rp rec_lig1.prmtop -lp
lig2.prmtop -y complex.nc -yr rec_lig1.nc -yl lig2.nc > process.log&
The result showed very large EInt value (BOND: 1053.0602, ANGLE: 55.7940,
DIHED: -437.3012). When I just calculate the binding free energy for the
receptor and lig1, the results are reasonable (BOND: 1.2874, ANGLE: 26.8525,
DIHED: 97.8098). The command is: ...... -sp rec_lig1_water.prmtop -cp
rec_lig1.prmtop -rp rec.prmtop -lp lig1.prmtop -y rec_lig1.nc -yr rec.nc -yl
lig1.nc
I wonder whether the three trajectory MMGBSA calculation is suitable for
calculating a complex with two molecules? Does anybody know how to calculate
the binding free energies for complex with two ligands, especially when the
binding of lig2 could induce large conformational changes?
Sincerely yours,
Cuiyl
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Received on Sun Apr 08 2018 - 02:00:02 PDT
