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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 6:51 AM, Josh Berryman <the.real.josh.berryman.gmail.com> wrote: >>>>I think there are still a couple issues. > > Yup, like not compiling. Just a heads up in case noone else has been > checking the cruise control. Here's the last bit of the log: > > " > mpif90 -DBINTRAJ -DEMIL -DMPI -c -O3 -mtune=native -ffree-form > -I/home/cc/cruisecontrol_amber/projects/Amber_parallel_gnu-4.4.6/include > -I/home/cc/cruisecontrol_amber/projects/Amber_parallel_gnu-4.4.6/include > -o pb_force.o pb_force.F90 > pb_force.F90:290.77: > > sa_init, sa_driver, sa_free, sa_free_mb, & > 1 > Error: Symbol 'saslave_init' referenced at (1) not found in module > 'solvent_accessibility' > make[3]: Leaving directory > `/home/cc/cruisecontrol_amber/projects/Amber_parallel_gnu-4.4.6/AmberTools/src/pbsa' > make[2]: Leaving directory > `/home/cc/cruisecontrol_amber/projects/Amber_parallel_gnu-4.4.6/src/sander' > make[1]: Leaving directory > `/home/cc/cruisecontrol_amber/projects/Amber_parallel_gnu-4.4.6/src' > " > > On 11/02/2014, 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-developers _______________________________________________ AMBER-Developers mailing list AMBER-Developers.ambermd.org http://lists.ambermd.org/mailman/listinfo/amber-developersReceived on Tue Feb 11 2014 - 15:30:08 PST