Is there nothing in _MMPBSA_*_nm.out to suggest a possible error?
On Thu, Jul 5, 2012 at 3:05 PM, bmartini <bmartini.ibt.unam.mx> wrote:
> Hello Jason,
>
> The err file does not give any information about why the entropy
> calculation is not accomplished but _MMPBSA_com_nm_traj_cpptraj.out gave
> me the following information:
>
> CPPTRAJ: Trajectory Analysis. V12.1
> ___ ___ ___ ___
> | \/ | \/ | \/ |
> _|_/\_|_/\_|_/\_|_
>
> INPUT: Reading Input from STDIN, type "go" to run, "quit" to exit:
> > [trajin _MMPBSA_complex.mdcrd.0 5 10 5]
> [_MMPBSA_complex.mdcrd.0] contains 13 frames.
> > [trajin _MMPBSA_complex.mdcrd.1 2 12 5]
> [_MMPBSA_complex.mdcrd.1] contains 13 frames.
> > [trajin _MMPBSA_complex.mdcrd.2 4 9 5]
> [_MMPBSA_complex.mdcrd.2] contains 12 frames.
> > [trajin _MMPBSA_complex.mdcrd.3 2 12 5]
> [_MMPBSA_complex.mdcrd.3] contains 12 frames.
> > [noprogress]
> noprogress: Progress bar will not be shown.
> > [outtraj _MMPBSA_complex_nm.mdcrd.0 onlyframes 1-3 nobox]
> > [outtraj _MMPBSA_complex_nm.mdcrd.1 onlyframes 4-5 nobox]
> > [outtraj _MMPBSA_complex_nm.mdcrd.2 onlyframes 6-7 nobox]
> > [outtraj _MMPBSA_complex_nm.mdcrd.3 onlyframes 8-9 nobox]
> >
> INPUT TRAJECTORIES:
> [_MMPBSA_complex.mdcrd.0] is an AMBER trajectory, Parm 0 (reading 2
> of 13)
> [_MMPBSA_complex.mdcrd.1] is an AMBER trajectory, Parm 0 (reading 3
> of 13)
> [_MMPBSA_complex.mdcrd.2] is an AMBER trajectory, Parm 0 (reading 2
> of 12)
> [_MMPBSA_complex.mdcrd.3] is an AMBER trajectory, Parm 0 (reading 3
> of 12)
> Coordinate processing will occur on 10 frames.
>
> PARAMETER FILES:
> 0: neura-sia.prmtop, 6018 atoms, 389 res, no box, 10 frames
>
> REFERENCE COORDS:
> No reference coordinates.
> No frames defined.
>
> OUTPUT TRAJECTORIES:
> No files.
>
> ACTIONS: Initializing 4 actions:
> 0: [outtraj _MMPBSA_complex_nm.mdcrd.0 onlyframes 1-3 nobox]
> Saving frames 1 2 3 OUTTRAJ: [_MMPBSA_complex_nm.mdcrd.0] is
> an AMBER trajectory, Parm 0: Writing frames 1 2 3
>
> 1: [outtraj _MMPBSA_complex_nm.mdcrd.1 onlyframes 4-5 nobox]
> Saving frames 4 5 OUTTRAJ: [_MMPBSA_complex_nm.mdcrd.1] is an
> AMBER trajectory, Parm 0: Writing frames 4 5
>
> 2: [outtraj _MMPBSA_complex_nm.mdcrd.2 onlyframes 6-7 nobox]
> Saving frames 6 7 OUTTRAJ: [_MMPBSA_complex_nm.mdcrd.2] is an
> AMBER trajectory, Parm 0: Writing frames 6 7
>
> 3: [outtraj _MMPBSA_complex_nm.mdcrd.3 onlyframes 8-9 nobox]
> Saving frames 8 9 OUTTRAJ: [_MMPBSA_complex_nm.mdcrd.3] is an
> AMBER trajectory, Parm 0: Writing frames 8 9
>
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> PARM [neura-sia.prmtop]: Setting up 4 actions.
> 0: [outtraj _MMPBSA_complex_nm.mdcrd.0 onlyframes 1-3 nobox]
> 1: [outtraj _MMPBSA_complex_nm.mdcrd.1 onlyframes 4-5 nobox]
> 2: [outtraj _MMPBSA_complex_nm.mdcrd.2 onlyframes 6-7 nobox]
> 3: [outtraj _MMPBSA_complex_nm.mdcrd.3 onlyframes 8-9 nobox]
> ----- [_MMPBSA_complex.mdcrd.0] (5-10, 5) -----
>
> ----- [_MMPBSA_complex.mdcrd.1] (2-12, 5) -----
>
> ----- [_MMPBSA_complex.mdcrd.2] (4-9, 5) -----
>
> ----- [_MMPBSA_complex.mdcrd.3] (2-12, 5) -----
>
> Read 10 frames and processed 10 frames.
>
> ACTION OUTPUT:
> OUTTRAJ: [_MMPBSA_complex_nm.mdcrd.0] Wrote 3 frames.
> OUTTRAJ: [_MMPBSA_complex_nm.mdcrd.1] Wrote 2 frames.
> OUTTRAJ: [_MMPBSA_complex_nm.mdcrd.2] Wrote 2 frames.
> OUTTRAJ: [_MMPBSA_complex_nm.mdcrd.3] Wrote 2 frames.
>
> DATASETS:
> There are no data sets set up for analysis.
>
>
> And the same happens with _MMPBSA_lig_nm_traj_cpptraj.out and
> _MMPBSA_rec_nm_traj_cpptraj.out.
>
> Best regards
>
>
>
> On Thu, 5 Jul 2012 13:05:16 -0400, Jason Swails
> <jason.swails.gmail.com> wrote:
> > Were there any error messages anywhere?
> >
> > On Thu, Jul 5, 2012 at 12:50 PM, bmartini <bmartini.ibt.unam.mx>
> > wrote:
> >
> >> Hello Amber users,
> >> I have had some problems running entropy calculations using nmode
> >> with
> >> the following parameters.
> >> &general
> >> endframe=50, keep_files=2,
> >> /
> >> &nmode
> >> nmstartframe=5, nmendframe=45,
> >> nminterval=5, nmode_igb=1, nmode_istrng=0.1,
> >> /
> >> Something that strikes my attention is that the same script did not
> >> give any problem when the size of my complex was 2600 atoms but for
> >> the
> >> case of 6010 atoms, the calculation is not accomplished and when I
> >> review the progress.log file, the next information appears:
> >> Running MMPBSA.MPI on 4 processors
> >> Reading command-line arguments and input files...
> >> Loading and checking parameter files for compatibility...
> >> cpptraj found! Using
> >> /global/home/egarciah_g/egarciah/amber12/bin/cpptraj
> >> ptraj found! Using
> >> /global/home/egarciah_g/egarciah/amber12/bin/ptraj
> >> mmpbsa_py_nabnmode found! Using
> >> /global/home/egarciah_g/egarciah/amber12/bin/mmpbsa_py_nabnmode
> >> Preparing trajectories for simulation...
> >> 50 frames were processed by cpptraj for use in calculation.
> >> 9 frames were processed by cpptraj for nmode calculations.
> >> Beginning nmode calculations with
> >> /global/home/egarciah_g/egarciah/amber12/bin/mmpbsa_py_nabnmode
> >> calculating complex contribution...
> >>
> >> It looks like the process had been stopped and err file did not
> >> give
> >> any information. Someone who knows how to deal with this problem?
> >> It
> >> could be a system size problem, couldnīt it?
> >>
> >> Thanks in advance
> >>
> >>
> >>
> >> _______________________________________________
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> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
>
>
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Jul 05 2012 - 12:30:04 PDT
