Hello Jason,
I'm sorry for having taken so long to write back. I ran again the
entropy calculation to check the _MMPBSA_*_nm.out because I had deleted
those files obtained in my last calculation. In this new calculation
_MMPBSA_complex_nm.out.0 files show the following information in the
last part of the file but they did not say anything about it.
Furthermore, an empty err file appears.
_MMPBSA_complex_nm.out.0
LS: i= 1 lhs_f= -0.0004508087 rhs_f= -9.0249913e-08
lhs_g= 2.051208e-07 rhs_g= 0.00081224922
LS: step= 1 it= 1
MIN: Iter = 283 NFunc = 7385 E = -2932.78178 RMSG =
8.8869033e-04
----------------------------------------------------------------
END: :-) E = -2932.78178 RMSG = 0.0008887
----Convergence Satisfied----
iter Total bad vdW elect nonpolar genBorn
frms
_MMPBSA_complex_nm.out.1
MIN: Iter = 318 NFunc = 7497 E = -2938.03139 RMSG =
2.5120250e-02
CG: It= 50 ( 1.065)q :-(
LS: i= 1 lhs_f= -0.15484949 rhs_f= -2.5814789e-05
lhs_g= 0.051740183 rhs_g= 0.30063872
LS: step= 0.77279832 it= 1
MIN: Iter = 319 NFunc = 7548 E = -2938.18625 RMSG =
2.9764896e-02
CG: It= 4 ( 0.497)q :-)
LS: i= 1 lhs_f= -0.020276009 rhs_f= -4.024484e-06
lhs_g= 0.00055294048 rhs_g= 0.036220356
LS: step= 1 it= 1
_MMPBSA_complex_nm.out.2
LS: i= 1 lhs_f= -0.00050996865 rhs_f= -1.0202919e-07
lhs_g= 6.9030469e-07 rhs_g= 0.00091826272
LS: step= 1 it= 1
MIN: Iter = 270 NFunc = 7014 E = -2947.41168 RMSG =
9.6431725e-04
----------------------------------------------------------------
END: :-) E = -2947.41168 RMSG = 0.0009643
----Convergence Satisfied----
iter Total bad vdW elect nonpolar genBorn
frms
_MMPBSA_complex_nm.out.3
LS: i= 1 lhs_f= -0.00051590644 rhs_f= -1.032233e-07
lhs_g= 5.088167e-07 rhs_g= 0.00092900971
LS: step= 1 it= 1
MIN: Iter = 264 NFunc = 7469 E = -2934.57520 RMSG =
9.7376181e-04
----------------------------------------------------------------
END: :-) E = -2934.57520 RMSG = 0.0009738
----Convergence Satisfied----
iter Total bad vdW elect nonpolar genBorn
frms
Greetings
On Thu, 5 Jul 2012 15:29:24 -0400, Jason Swails
<jason.swails.gmail.com> wrote:
> 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, couldn´t it?
>> >>
>> >> Thanks in advance
>> >>
>> >>
>> >>
>> >> _______________________________________________
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>> >> AMBER.ambermd.org
>> >> http://lists.ambermd.org/mailman/listinfo/amber
>> >>
>>
>>
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Received on Fri Jul 06 2012 - 10:00:03 PDT
