It looks like your system privileges may not allow you to use as much memory
as nmode requires. Ask your sysadmin about how much memory you are
permitted (or request more in your PBS/queue script).
The calculation is being killed right after the minimization is complete and
the normal mode calculation begins. It is this part of the calculation that
requires the most memory and it appears as though something outside of
MMPBSA is killing the process.
Hope this helps,
Jason
On Thu, Aug 4, 2011 at 12:10 PM, manikanthan bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> Hi All,
> I am using MMPBSA script in serial, of AmberTools1.5 for entropy
> calculations. I have successfully calculated PBSA and GBSA for the complex
> system. But when I am performing nab calculations it is giving following
> error in the progress.log
>
> Reading command-line arguments and input files...
> Loading and checking parameter files for compatibility...
> Warning: RADIUS_SET cannot be found in your prmtop files!
> ptraj found! Using /home/srg/mhb75/Download/amber11/bin/ptraj
> nmode program found! Using
> /home/srg/mhb75/Download/amber11/bin/mmpbsa_py_nabnmode
> Preparing trajectories for simulation...
> 1 frames were read in and processed by ptraj for use in calculation.
>
> Beginning nmode calculations with mmpbsa_py_nabnmode...
> Calculating normal modes for 1 frames
>
> calculating complex contribution for frame 0
> sh: line 1: 27098 Killed
> /home/srg/mhb75/Download/amber11/bin/mmpbsa_py_nabnmode
> _MMPBSA_complex_nm.pdb.1 complex_nw.prmtop 10000 0.001 "ntpr=10000, diel=C,
> kappa=0.103951911959, cut=1000, gb=1, dielc=4.0, temp0=298.15, wcons=0" >>
> _MMPBSA_complex_nm.out
> Error: error during mmpbsa_py_nabnmode calculations!
> NOTE: All files have been retained for debugging purposes. Type MMPBSA.py
> --clean to erase these files.
>
>
> The script is getting crashed when the complex minization is done.
> The _MMPBSA_complex_nm.out last lines looks like
>
> LS: step= 1 it= 1
> MIN: It= 280 nfunc= 8235 E= -3850.77578 ( 1.38e-03)
> CG: It= 50 ( 1.018)q :-(
> LS: i= 1 lhs_f= -0.0010710421 rhs_f= -2.1445542e-07
> lhs_g= 2.8783911e-06 rhs_g= 0.0019300988
> LS: step= 1 it= 1
> MIN: It= 281 nfunc= 8286 E= -3850.77685 ( 1.29e-03)
> CG: It= 50 ( 1.014)q :-(
> LS: i= 1 lhs_f= -0.001007292 rhs_f= -2.0161816e-07
> lhs_g= 1.6685223e-06 rhs_g= 0.0018145635
> LS: step= 1 it= 1
> MIN: It= 282 nfunc= 8337 E= -3850.77786 ( 1.19e-03)
> CG: It= 50 ( 0.905)q :-(
> LS: i= 1 lhs_f= -0.00081047998 rhs_f= -1.6216577e-07
> lhs_g= 1.322888e-07 rhs_g= 0.0014594919
> LS: step= 1 it= 1
> MIN: It= 283 nfunc= 8388 E= -3850.77867 ( 9.95e-04)
> ----------------------------------------------------------------
> FIN: :-) E= -3850.78 ( 0.001)
>
> ----Convergence Satisfied----
>
> iter Total bad vdW elect nonpolar genBorn
> frm
>
>
>
>
> I am also performing nmode calculations for 50 snapshots for other systems
> and they are working fine. But for the above system even for one snapshot
> the script is getting crashed.
>
>
>
>
> Thanks,
> mani
> _______________________________________________
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> 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 Thu Aug 04 2011 - 09:30:04 PDT
