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-- Ray Luo, Ph.D. Professor, Biochemistry, Molecular Biophysics, and Biomedical Engineering University of California, Irvine, CA 92697-3900 On Tue, Feb 11, 2014 at 5:32 AM, Jason Swails <jason.swails.gmail.com> wrote: > On Mon, 2014-02-10 at 18:18 -0800, Ray Luo, Ph.D. wrote: >> The sander/pbsa interface issue has been fixed and pushed ... > > I think there are still a couple issues. The MMPBSA.py tests (which I > just got working again) are now failing on the sander/PBSA interface. > > This is the error I'm getting from the _MMPBSA_complex_pb.mdout output > file: > > File generated by MMPBSA.py > &cntrl > nsnb=99999, ipb=2, ntb=0, cut=999.0, > imin=5, idecomp=1, igb=10, > / > &pb > istrng=150.0, maxitn=1000, > fillratio=4.0, radiopt=1, > / > Residues considered as REC > RRES 4 6 > END > Residues considered as LIG > LRES 1 3 > END > Residues to print > RES 1 6 > END > END > > -------------------------------------------------------------------------------- > 1. RESOURCE USE: > -------------------------------------------------------------------------------- > > | Flags: > PB Bomb in pb_read(): ipb can only be larger than or equal to 1. > > > So it seems that somewhere the value if ipb (which is set to 2 in the > input file) is not being propagated to the PB part? I can't find an > obvious place where this is happening and this input file has not > changed since the AmberTools 13 release (when it worked with Amber 12). > You can run the 07_Comprehensive test in AmberTools/test/mmpbsa_py for a > reproducible case. > > Thanks! > Jason > > -- > Jason M. Swails > BioMaPS, > Rutgers University > Postdoctoral Researcher > > > _______________________________________________ > AMBER-Developers mailing list > AMBER-Developers.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber-developers _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Tue Feb 11 2014 - 10:00:07 PST