Hello all
I want to calculate MMGBSA from dcd file. I have converted it to .mdcrd
using cpptraj.
cpptraj -p complex-box.prmtop -y sim1_14.dcd -x sim1_14_complex.mdcrd
Then using,
MMPBSA.py -i mmpbsa.in -o FINAL_RESULTS_MMPBSA_20_frames.dat -sp
complex-box.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop
-y sim1_14_complex.mdcrd
###MMPBSA.in#############
Input file for running PB and GB in serial
&general
endframe=20, keep_files=2,
/
&gb
igb=2, saltcon=0.100,
/
&pb
istrng=0.100,
/
################################
But getting error,
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/apps/amber/amber12/bin/mmpbsa_py_energy
cpptraj found! Using /opt/apps/amber/amber12/bin/cpptraj
Preparing trajectories for simulation...
20 frames were processed by cpptraj for use in calculation.
Beginning GB calculations with /opt/apps/amber/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with /opt/apps/amber/amber12/bin/mmpbsa_py_energy
calculating complex contribution...
CalcError: /opt/apps/amber/amber12/bin/mmpbsa_py_energy failed with prmtop
complex.prmtop!
Exiting. All files have been retained.
Can someone suggest?
Regards
Shivangi Agarwal
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Received on Fri Aug 16 2019 - 01:30:04 PDT
