I have stripped ions and water from the complex1_solv.prmtop using
ante-MMPBSA.py. and created the nc files without the water and ion
information. Then I had an error since the number of atoms in complex was
not ligand+ receptor. So I removed ions from the receptor and tried again.
The job started running but it has been stuck in the following line for
like 3 hours. The nc file now has no ions or water. Does it usually take
this long to complete the mmpbsa calculation?
MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -cp
dry.complex1_sol.prmtop -rp rec.prmtop -lp ligand.prmtop -y *.nc
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /apps/amber18/bin/mmpbsa_py_energy
cpptraj found! Using /apps/amber18/bin/cpptraj
mmpbsa_py_nabnmode found! Using /apps/amber18/bin/mmpbsa_py_nabnmode
Preparing trajectories for simulation...
28001 frames were processed by cpptraj for use in calculation.
28001 frames were processed by cpptraj for nmode calculations.
Running calculations on normal system...
Beginning GB calculations with /apps/amber18/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with /apps/amber18/bin/mmpbsa_py_energy
calculating complex contribution...
Warning: inp=1 was old default
Warning: cavity_surften=0.0378 not recommended for inp=1, switching to
inp=1 default value: 0.0050
Warning: cavity_offset=-0.5692 not recommended for inp=1, switching to
inp=1 default value: 0.000
Warning: sprob=.557 not recommended for inp=1, switching to inp=1 default
value: 1.400
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Received on Tue Feb 18 2020 - 05:30:01 PST
