I have done Amber12 simulation for a preotein-protein complex with explicit solvent. I have used FF12SB force field. Now I am trying to perform MMPBSA calculation with the following script:
General MMPBSA.py input file
&general
startframe=1, endframe=100, interval=50, receptor_mask=:1-64, ligand_mask=:65-146,
keep_files=0, verbose=1, strip_mask=:WAT:Na+,
/
&gb
igb=5, saltcon=0.1,
/
&pb
istrng=0.1, exdi=80, indi=1.0,
inp=2, cavity_surften=0.0378, cavity_offset=-0.5692,
fillratio=4, scale=2.0,
linit=1000, prbrad=1.4, radiopt=1,
/
It returns with the following error:
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /opt/software/Amber/12--Intel-12.1.2.273/bin/mmpbsa_py_energy
cpptraj found! Using /opt/software/Amber/12--Intel-12.1.2.273/bin/cpptraj
Preparing trajectories for simulation...
2 frames were processed by cpptraj for use in calculation.
Beginning GB calculations with /opt/software/Amber/12--Intel-12.1.2.273/bin/mmpbsa_py_energy
calculating complex contribution...
calculating receptor contribution...
calculating ligand contribution...
Beginning PB calculations with /opt/software/Amber/12--Intel-12.1.2.273/bin/mmpbsa_py_energy
calculating complex contribution...
CalcError: /opt/software/Amber/12--Intel-12.1.2.273/bin/mmpbsa_py_energy failed with prmtop ../cplx_conf.prmtop!
PB Bomb in pb_aaradi(): No radius assigned for atom 14 CB 2C
Exiting. All files have been retained.
ATOM 14 is a Ser residue CB atoms. I am wondering why the program cannot recognize such a obvious atom type. Given topology file works fine with all other ptraj input or visualizing purposes.
Please let me know if you have any clue or how to overcome this problem.
With best regards,
Rahul
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Received on Mon Dec 03 2012 - 12:00:02 PST
