Re: [AMBER] error: "STOP PMEMD terminated abnormally"

From: Hirdesh Kumar <>
Date: Wed, 13 Aug 2014 17:57:00 +0200

I also faced the same problem. I ran 100ns simulation of my
protein-ligand-ion complex in TIP3P. I found that the rmsd value for ligand
is not stable so thought of continuing the simulation. But I can not use
the restart file.

I got following error:
 ERROR: I could not understand line 22288
 119.5803932 241.7497484-572.4462595

I opened the previous restart file and checked for this line. I found that
usually there are 6 coordinates in a line (for 2 atoms, if I am not wrong).
But in the error line there is only 3 coordinate information..

  32.4272362 107.0995698 73.2442804 31.4632046 106.0229371 72.7942916
 120.3886214 242.0088540-572.8888241 121.0825779 241.7930826-572.2658482
 119.5803932 241.7497484-572.4462595
  -0.0167718 -0.0424197 -0.0394365 0.1475965 0.5324544 0.2035670
   0.2566837 -0.1595890 -0.0562660 -0.0466537 0.0079685 -0.1094048

I tried to generate the pdb file from last restart file (using ambpdb) but
it also showed some error.

As an alternative, I took previous trajectory file (prod1.crd) and I tried
to generate the restart file after 50 ns simulation. I managed to generate
the restart file (also ambpdb worked with with this new restart).

BUT, when I restarted my simulation with this restart file, I got following

*ERROR: I could not find enough velocities in restart1.rst*

As Dac suggested, I can use the netcdf format in future. But please let me
know how to restart this simulation 100ns onward???


> I found topic *STOP PMEMD Terminated Abnormally *on the mailing list, but
> > havent found the solution for my case. Could you please help take a look?
> >
> > I have run MD simulation (85ns) for my model with an interval of 5ns for
> > each run.
> > I got "*STOP PMEMD Terminated Abnormally*!", and the output file gave me
> an
> > error:
> >
> > *ERROR: I could not understand line 29789*
> > *-327.9383128 54.8526179-268.4522643*
> Look for any '*' characters in the file. The line number reported is not
> always the place where the error really occurs. Also, check the size of
> the
> file that has a problem vs. the size of earlier files that worked OK.
> And, of
> course, look for any clues in the mdout file from the earlier run that
> would
> point to a problem.
> Since you've had other similar problems, I'd suggest setting ntxo=2, to use
> the netcdf restart format.
> ....good luck....dac
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Received on Wed Aug 13 2014 - 09:00:02 PDT
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