Dear AMBER users,
I'm trying to run an MMPBSA calculation on a system consisting of a lipid membrane (treated as receptor) and a peptide (treated as ligand).
I've double checked my prmtops several times and made sure that they are compatible. My input file (MMPBSA.in) is as follows:
MMPBSA
&general
startframe=4000, endframe=5000, interval=10, receptor_mask=":PS", ligand_mask=":ALA,:ARG,:ASP,:GLN,:GLU,:GLY,:ILE,:LEU,:LYS,:MET,:NME,:PHE,:PRO,:SER,:S2P,:THR,:VAL",
verbose=1, strip_mask=":WAT,:Na+",
/
&pb
istrng=0.000,
/
However, when I try to run MMPBSA.py, an error is encountered. I couldn't find the error in the archive or when I tried to google it.
[ask054.nc-med232209 test_mmpbsa]$ MMPBSA.py -O -i MMPBSA.in -o test_mmpbsa.dat -sp POPS_pTHpep.prmtop -cp POPS_pTHpep_vac.prmtop -rp pPOPS_vac.prmtop -lp pTHpep_vac.prmtop -y POPS_pTHpep_prod.nc
Reading command-line arguments and input files...
Loading and checking parameter files for compatibility...
mmpbsa_py_energy found! Using /usr/local/amber/bin/mmpbsa_py_energy
cpptraj found! Using /usr/local/amber/bin/cpptraj
Preparing trajectories for simulation...
101 frames were processed by cpptraj for use in calculation.
Beginning PB calculations with /usr/local/amber/bin/mmpbsa_py_energy
calculating complex contribution...
Error: Unknown PB optonn bcopt!CalcError: /usr/local/amber/bin/mmpbsa_py_energy failed with prmtop POPS_pTHpep_vac.prmtop!
Exiting. All files have been retained.
It seems to be complaining about the bcopt option in _MMPBSA_pb.mdin, even though the default option in the AmberTools manual (bcopt = 5) is used. Can someone help me figure out what's going on?
Thanks in advance.
Best regards,
Åge Aleksander Skjevik
Department of Biomedicine
University of Bergen, Norway
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Received on Thu Feb 23 2012 - 10:00:02 PST
