Your normal mode calculations are not working.
Check the intermediate nmode output files for error messages. Possible
explanations are that your machine does not have enough memory or snapshots
are not minimizing to within tolerable limits for running normal mode
calculations, in which case you would need to increase the maximum number
of minimization steps.
If the minimization is the problem, I would suggest trying MMPBSA.py, since
it uses the xmin minimizer which does a better job than the conjugate
gradient method implemented in sander (used by mm_pbsa.pl). If memory is
the issue, there's little that can be done outside of finding a machine
with more memory to run on.
HTH,
Jason
On Wed, Aug 1, 2012 at 1:36 PM, manikanthan bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> Dear All,
>
> I am trying to calculate entropy contribution of the protein using
> ambe12 mmpbsa.pl script. The following is the input file.
>
> .GENERAL
> PREFIX snapshot
> PATH ./
> COMPLEX 0
> RECEPTOR 1
> LIGAND 0
> RECPT ./hAChE.prmtop
> GC 1
> AS 0
> DC 0
> MM 0
> GB 0
> PB 0
> MS 0
> NM 1
> .MAKECRD
> BOX YES
> NTOTAL 58507
> NSTART 1
> NSTOP 1000
> NFREQ 1000
> NUMBER_LIG_GROUPS 0
> LSTART 0
> LSTOP 0
> NUMBER_REC_GROUPS 1
> RSTART 1
> RSTOP 8297
> .NM
> DIELC 4
> MAXCYC 20000
> DRMS 0.001
> IGB 0
> PROC 2
> .TRAJECTORY
> TRAJECTORY ./RES_md10.mdcrd
> .PROGRAMS
>
>
> The job is getting executed but nothing is written to the output and
> the log file displaying the following error
>
> =>> Doing statistics
> =>> Reading input
> =>> Reordering files
> Final order:
> 1. snapshot_rec.all.out: -
> =>> Reading files
> Reading snapshot_rec.all.out
> WARNING: Missing SROT for NM in 0 -> Taken from -1
> For details see:
>
> http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
> WARNING: Missing STOT for NM in 0 -> Taken from -1
> For details see:
>
> http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
> WARNING: Missing STRA for NM in 0 -> Taken from -1
> For details see:
>
> http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
> WARNING: Missing SVIB for NM in 0 -> Taken from -1
> For details see:
>
> http://ambermd.org/Questions/mm_pbsa.html#check_completeness_missing_var_taken_from
> =>> Values of parameters
> TEMP = 300
> R = 8.314
> =>> Treat special parameters
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber12/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber12/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber12/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
> Use of uninitialized value in multiplication (*) at
> /usr/local/amber12/src/mm_pbsa/mm_pbsa_statistics.pm line 1457.
> =>> Calc missing parameters
> =>> Calc average and stddev
> =>> Print output to snapshot_statistics.out
> =>> Print output (snap) to snapshot_statistics.out.snap
>
> thanks,
> mani
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Aug 01 2012 - 11:00:04 PDT
