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-- Guqin SHI PhD Candidate in Medicinal Chemistry and Pharmacognosy College of Pharmacy The Ohio State University Columbus, OH, 43210 On Sat, Jul 8, 2017 at 11:52 AM, Elvis Martis <elvis.martis.bcp.edu.in> wrote: > HI, > As you can see the warning for pb_radii. > It is worthwhile to inp=2 and compare your results. > Also check the appropriate internal dielectric constant for you, the > default is 1. you can explore 2 and 4 depending on how polar or hydrophobic > your binding site is. You can refer to this paper > http://pubs.acs.org/doi/abs/10.1021/ci100275a which will guide you > through the selection. > > Best Regards > Elvis Martis > Mumbai, INDIA. > > ________________________________________ > From: Guqin Shi <shi.293.osu.edu> > Sent: 08 July 2017 20:13:25 > To: AMBER Mailing List > Subject: Re: [AMBER] MMPBSA.py.MPI errors with prmtop files on PBS platform > > Hi Elvis, > > I do have the radiopt=0 in the input. Please see below: > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > MM-PBSA with original PB solvation model (inp=1) > > &general > > startframe=7002, interval=5, endframe=7500, verbose=2, keep_files=1, > debug_printlevel=2, > > / > > &pb > > istrng=0.15, inp=1, cavity_offset=0.92, cavity_surften=0.00542,radiopt=0 > > / > > &decomp > > idecomp=1, dec_verbose=3 > > / > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > > I tried increasing the memory being allocated to each cpu... this time it > seems finished. But the final results file they are huge positive numbers, > it also reminded that "WARNING: INCONSISTENCIES EXIST WITHIN INTERNAL > POTENTIAL > TERMS. THE VALIDITY OF THESE RESULTS ARE HIGHLY QUESTIONABLE" > I am wondering is there something I need to change for default to get > correct results? > > In one of the mdout temporary file, there is such a line: > > | Flags: > > PB Warning in pb_read(): sprob=0.557 is optimized for inp=2 and should > not be used with inp=1. It has been reset to 1.4. > > The program changed sprob for me. But other than that, I don't know where > other warnings are... > > > Thanks! > > Guqin > > On Fri, Jul 7, 2017 at 11:39 PM, Elvis Martis <elvis.martis.bcp.edu.in> > wrote: > > > Hi, > > Are you using Bondi radii? In case you have set the default PB radii as > > mbondi2 or mbondi3 in leap, your need to set "radiopt=0" (=1 is default). > > Try this > > 1) in your &general section, use_sander=1, > > 2) in your &pb section, inp=2, radiopt=0, > > > > Best Regards > > Elvis Martis > > Mumbai, INDIA. > > > > ________________________________________ > > From: Guqin Shi [shi.293.osu.edu] > > Sent: 08 July 2017 04:17 > > To: AMBER Mailing List > > Subject: [AMBER] MMPBSA.py.MPI errors with prmtop files on PBS platform > > > > Dear all, > > > > I am running MMPBSA.py.MPI on a computing cluster with PBS platform. > > Recently I got errors that the MMPBSA.py.MPI failed with the > > complex.prmtop... I attached the error output at the end. > > > > I highlighted the error message. But the problem is that, the same prmtop > > file is been used for all the trajectories. I've been working on this > > system for the past few weeks. The first 50 ns of trajectories were all > > calculated with MMPBSA.py.MPI using same prmtop and same script, nothing > > went wrong. > > > > And also, the trajectories were prepared by cpptraj successfully (I > > indicated different starting frames with interval at 5); therefore I > > believe the prmtop file itself isn't a problem...(Although I did > re-prepare > > it again, apparently it didn't help)... Has anybody encountered the same > > problem before? > > > > The hexamer I am working on is a huge system containing 1300 residues. I > > have imaged and centered on chains to make sure all coordinates are > written > > correctly. By inspecting the trajectories frame by frame, they all look > > fine and nothing deviates... Will that be a memory issue or some how? > What > > tortures me is that the previous 50 ns trajectories of MMPBSA calculation > > were finished successfully...I have no idea why now it's proceeding to > > around 75 ns and things get weird... > > > > Any thoughts and tips would help! Please let me know if more information > is > > needed!! Thank you! > > > > -Guqin > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > Loading and checking parameter files for compatibility... > > sander found! Using /usr/local/amber/amber14/bin/sander > > cpptraj found! Using /usr/local/amber/amber14/bin/cpptraj > > Preparing trajectories for simulation... > > 100 frames were processed by cpptraj for use in calculation. > > > > Running calculations on normal system... > > > > Beginning PB calculations with /usr/local/amber/amber14/bin/sander > > calculating complex contribution... > > File "/usr/local/amber/amber14/bin/MMPBSA.py.MPI", line 96, in > <module> > > app.run_mmpbsa() > > File "/usr/local/amber/amber14/bin/MMPBSA_mods/main.py", line 218, in > > run_mmpbsa > > self.calc_list.run(rank, self.stdout) > > File "/usr/local/amber/amber14/bin/MMPBSA_mods/calculation.py", line > 79, > > in run > > calc.run(rank, stdout=stdout, stderr=stderr) > > File "/usr/local/amber/amber14/bin/MMPBSA_mods/calculation.py", line > > 416, > > in run > > self.prmtop) + '\n\t'.join(error_list) + '\n') > > *CalcError: /usr/local/amber/amber14/bin/sander failed with prmtop > > ../../Hexamer_complex_mbondi2.prmtop!* > > > > > > Error occured on rank 17. > > Exiting. All files have been retained. > > [cli_17]: aborting job: > > application called MPI_Abort(MPI_COMM_WORLD, 1) - process 17 > > > > ============================================================ > > ======================= > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > > = PID 6537 RUNNING AT n0148 > > = EXIT CODE: 1 > > = CLEANING UP REMAINING PROCESSES > > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > > ============================================================ > > ======================= > > [proxy:0:0.n0153.ten.osc.edu] HYD_pmcd_pmip_control_cmd_cb > > (pm/pmiserv/pmip_cb.c:885): assert (!closed) failed > > [proxy:0:0.n0153.ten.osc.edu] HYDT_dmxu_poll_wait_for_event > > (tools/demux/demux_poll.c:76): callback returned error status > > [proxy:0:0.n0153.ten.osc.edu] main (pm/pmiserv/pmip.c:206): demux engine > > error waiting for event > > > > ----------------------- > > Resources requested: > > nodes=2:ppn=12 > > ----------------------- > > Resources used: > > cput=00:40:04 > > walltime=00:02:51 > > mem=91.644 GB > > vmem=198.941 GB > > ----------------------- > > Resource units charged (estimate): > > 0.114 RUs > > ----------------------- > > > > +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ > > > > > > -- > > Guqin SHI > > PhD Candidate in Medicinal Chemistry and Pharmacognosy > > College of Pharmacy > > The Ohio State University > > Columbus, OH, 43210 > > _______________________________________________ > > 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 > > > > > > -- > Guqin SHI > PhD Candidate in Medicinal Chemistry and Pharmacognosy > College of Pharmacy > The Ohio State University > Columbus, OH, 43210 > _______________________________________________ > 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 > -- Guqin SHI PhD Candidate in Medicinal Chemistry and Pharmacognosy College of Pharmacy The Ohio State University Columbus, OH, 43210 _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Sat Jul 08 2017 - 13:30:02 PDT