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-- Best Regards, Qinghua On Thu, Dec 15, 2011 at 10:30 PM, Jason Swails <jason.swails.gmail.com>wrote: > You're running a decomposition analysis with MMPBSA.py, but not with > mm_pbsa.pl. Decomposition adds significant time to the calculation > (especially for PB, I believe). > > HTH, > Jason > > On Thu, Dec 15, 2011 at 3:44 PM, Qinghua Liao <fantasticqhl.gmail.com > >wrote: > > > Dear Jason, > > > > Thanks again. Here is my input file for the mm_pbsa.pl calculation: > > > > .GENERAL > > # > > VERBOSE 0 > > PARALLEL 8 > > # > > PREFIX snapshot > > PATH ../snapshots/ > > START 1 > > STOP 400 > > OFFSET 1 > > # > > COMPLEX 1 > > RECEPTOR 1 > > LIGAND 1 > > # > > COMPT ../com.prmtop > > RECPT ../rec.prmtop > > LIGPT ../lig.prmtop > > # > > GC 0 > > AS 0 > > DC 0 > > # > > MM 1 > > GB 1 > > PB 1 > > MS 1 > > # > > NM 0 > > # > > > > > ################################################################################ > > .PB > > # > > PROC 2 > > REFE 0 > > INDI 1.0 > > EXDI 80.0 > > SCALE 2 > > LINIT 1000 > > PRBRAD 1.4 > > ISTRNG 0.10 > > RADIOPT 1 > > INP 1 > > # > > SURFTEN 0.00542 > > SURFOFF -1.008 > > # > > IVCAP 0 > > CUTCAP -1.0 > > XCAP 0.0 > > YCAP 0.0 > > ZCAP 0.0 > > # > > > > > ################################################################################ > > .MM > > # > > DIELC 1.0 > > # > > > > > ################################################################################ > > .GB > > # > > # > > IGB 5 > > GBSA 2 > > SALTCON 0.10 > > EXTDIEL 80.0 > > INTDIEL 1.0 > > # > > SURFTEN 0.0072 > > SURFOFF 0.00 > > # > > > > > ################################################################################ > > .MS > > # > > # > > PROBE 0.0 > > # > > > > > ################################################################################ > > .PROGRAMS > > # > > # Additional program executables can be defined here > > # > > # > > > > > ################################################################################ > > > > How should I check the temporary files? In mm_pbsa.pl's calculation, I > can > > check the output files for the process, but in the python version, how > > should I checnk the process? > > > > Right now, I guess that the calculation was died, however, the sander are > > still working. Is it possible for the python version? > > Here are the temporary files in the working folder: > > > > _MMPBSA_avgcomplex.pdb _MMPBSA_comtraj.in.0 > > _MMPBSA_ligandinpcrd.in _MMPBSA_pb_decomp_rec.mdin > > _MMPBSA_ptraj5.out _MMPBSA_receptor.pdb > > _MMPBSA_cenptraj.in _MMPBSA_dummycomplex.inpcrd.1 > > _MMPBSA_ligand.mdcrd _MMPBSA_ptraj1.out > > _MMPBSA_ptraj6.out _MMPBSA_rectraj.in > > _MMPBSA_complex_gb.mdout.0 _MMPBSA_dummyligand.inpcrd.1 > > _MMPBSA_ligand.mdcrd.0 _MMPBSA_ptraj1.out.0 mmpbsa_py.in > > _MMPBSA_rectraj.in.0 > > _MMPBSA_complexinpcrd.in _MMPBSA_dummyreceptor.inpcrd.1 > > _MMPBSA_ligand.pdb _MMPBSA_ptraj2.out > > _MMPBSA_receptor_gb.mdout.0 _MMPBSA_.restrt.0 > > _MMPBSA_complex.mdcrd _MMPBSA_gb_decomp_com.mdin > > _MMPBSA_ligtraj.in _MMPBSA_ptraj2.out.0 > > _MMPBSA_receptorinpcrd.in mpd.hosts > > _MMPBSA_complex.mdcrd.0 _MMPBSA_gb_decomp_lig.mdin > > _MMPBSA_ligtraj.in.0 _MMPBSA_ptraj3.out > > _MMPBSA_receptor.mdcrd nohup.out > > _MMPBSA_complex_pb.mdout.0 _MMPBSA_gb_decomp_rec.mdin > > _MMPBSA_pb_decomp_com.mdin _MMPBSA_ptraj3.out.0 > > _MMPBSA_receptor.mdcrd.0 > > _MMPBSA_complex.pdb _MMPBSA_ligand_gb.mdout.0 > > _MMPBSA_pb_decomp_lig.mdin _MMPBSA_ptraj4.out > > _MMPBSA_receptor_pb.mdout.0 > > > > > > It seems no change for sometime now. I am going to kill one and redo it. > > Thanks! > > > > > > Best Regards, > > > > Qinghua > > > > > > > > On Thu, Dec 15, 2011 at 7:50 PM, Jason Swails <jason.swails.gmail.com > > >wrote: > > > > > What was your mm_pbsa.pl input file? Are temporary files (_MMPBSA_*) > > > still > > > being written to for MMPBSA.py? > > > > > > On Thu, Dec 15, 2011 at 11:21 AM, Qinghua Liao <fantasticqhl.gmail.com > > > >wrote: > > > > > > > Dear amber users, > > > > > > > > Is it very slow for calculating binding energy and decomposition > > > > simultaneously? It has been more than 24 hours for the calculation > > using > > > 16 > > > > cores' MMPBSA.MPI, and it has already finished using 8 core's > > > > mm_pbsa.plfor the calculation of binding energy. Here is the input > > > > file: > > > > > > > > &general > > > > startframe=1, endframe=400, interval=1, > > > > verbose=1, keep_files=1, > > > > / > > > > &gb > > > > igb=5, saltcon=0.10, surften=0.0072, surfoff=0.00, > > > > / > > > > &pb > > > > indi=1.0, exdi=80.0, scale=2.0, linit=1000, prbrad=1.4, > > > > inp=1, istrng=0.10, cavity_surften=0.00542, cavity_offset=-1.008, > > > > fillratio=4.0, > > > > / > > > > &decomp > > > > idecomp=2, dec_verbose=3, > > > > / > > > > > > > > I guess that there may be some problem with my input file, could > > someone > > > > give me a suggestion? Thanks very much! > > > > > > > > -- > > > > Best Regards, > > > > > > > > Qinghua > > > > _______________________________________________ > > > > AMBER mailing list > > > > AMBER.ambermd.org > > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > > > > > > > > > > > -- > > > Jason M. Swails > > > Quantum Theory Project, > > > University of Florida > > > Ph.D. Candidate > > > 352-392-4032 > > > _______________________________________________ > > > AMBER mailing list > > > AMBER.ambermd.org > > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > _______________________________________________ > > AMBER mailing list > > AMBER.ambermd.org > > http://lists.ambermd.org/mailman/listinfo/amber > > > > > > -- > Jason M. Swails > Quantum Theory Project, > University of Florida > Ph.D. Candidate > 352-392-4032 > _______________________________________________ > AMBER mailing list > AMBER.ambermd.org > http://lists.ambermd.org/mailman/listinfo/amber > _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Thu Dec 15 2011 - 23:00:02 PST