What version of MMPBSA.py are you using? It should be listed at the top of
the MMPBSA.py source file.
Also, do all of the MMPBSA.py and pbsa tests pass in the test directory?
-Bill
On Thu, Feb 23, 2012 at 12:49 PM, Åge Skjevik <aage.dark.hotmail.com> wrote:
>
> 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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>
--
Bill Miller III
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-6715
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Received on Fri Feb 24 2012 - 13:00:02 PST
