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, couldn´t it?
>>
>> Thanks in advance
>>
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
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Received on Thu Jul 05 2012 - 12:30:03 PDT
