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
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Received on Sat Jul 08 2017 - 09:00:02 PDT
