Dear All,
I try to calculate binding free energy between the protein-ligand complex. In my case during the PB calculation, it shows the length error,
(i.e) length mismatch in energy vectors. Help me to solve the problem. In the following I give the detail about the error during the calcualtion.
[Jeyaram.DBTSASKV 2]$ MMPBSA.py -O -i 1.in -o 1.dat -sp 1.prmtop -cp complex.prmtop -rp protein.prmtop -lp ligand.prmtop -y md2.nc
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /usr/local/bin/amber16/bin/mmpbsa_py_energy
cpptraj found! Using /usr/local/bin/amber16/bin/cpptraj
Preparing trajectories for simulation...
10 frames were processed by cpptraj for use in calculation.
Running calculations on normal system...
Beginning GB calculations with /usr/local/bin/amber16/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with /usr/local/bin/amber16/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
File "/usr/local/bin/amber16/bin/MMPBSA.py", line 108, in <module>
app.parse_output_files()
File "/usr/local/bin/amber16/lib/python2.7/site-packages/MMPBSA_mods/main.py", line 944, in parse_output_files
self.INPUT['verbose'], self.using_chamber)
File "/usr/local/bin/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", line 1007, in __init__
self.delta2()
File "/usr/local/bin/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", line 1234, in delta2
self.com.fill_composite_terms()
File "/usr/local/bin/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", line 372, in fill_composite_terms
self.data[component] = self.data[key] + self.data[component]
File "/usr/local/bin/amber16/lib/python2.7/site-packages/MMPBSA_mods/amber_outputs.py", line 61, in __add__
raise LengthError('length mismatch in energy vectors')
LengthError: length mismatch in energy vectors
Exiting. All files have been retained.
[Jeyaram.DBTSASKV 2]$
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Received on Wed Jan 17 2018 - 04:00:03 PST
