Re: [AMBER] TrajError: Could not find number of frames in .mdcrd

From: maryam azimzadehirani <>
Date: Mon, 8 Aug 2016 15:27:58 +0800

Sorry for not being specific.
I did load the trajectory in cpptraj and it read 5000 frames successfully.
I spent some more time on those files, one issue which I think might cause
a problem is that my receptor is glycosylated. I generated the initial
topology file with this order: 1. Receptor 2.ligand 3.glycans. Then I ran
Now that I am trying to run binding energy calculation, I was getting the
error that I explained in the previous email even though I specified
receptor mask (receptor+glycans) and ligand mask

After more reading on the similar errors I tried three trajectory approach,
were I used strip command to have trajectories of receptor, ligand and
complex, this is the input I used for receptor trajectory
trajin mmgbsa_150_200_reimage.mdcrd
strip :615-661
strip :WAT
strip :Na+
trajout mmgbsa_150_200_receptor_not_NA.mdcrd netcdf

then I removed mask in the input file and used: -O -i -o FINAL_RESULTS_MMPBSA.dat -cp
EGF_EGFR_no_wat.prmtop -rp EGFR_gly_no_wat.prmtop -lp EGF_no_wat.prmtop -yr
mmgbsa_150_200_receptor_not_NA.mdcrd -yl
mmgbsa_150_200_ligand_not_NA2.mdcrd -y mmgbsa_150_200_complex_not_NA.mdcrd

Now I am getting this error:

Loading and checking parameter files for compatibility...
  File "/usr/local/packages/amber14/bin/", line 94, in <module>
  File "/usr/local/packages/amber14/amber14/bin/MMPBSA_mods/", line
572, in loadcheck_prmtops
    FILES.receptor_prmtop, FILES.ligand_prmtop)
  File "/usr/local/packages/amber14/amber14/bin/MMPBSA_mods/",
line 109, in __init__
  File "/usr/local/packages/amber14/amber14/bin/MMPBSA_mods/",
line 868, in _validate
    raise PrmtopError('Complex natom != receptor natom + ligand natom')
PrmtopError: Complex natom != receptor natom + ligand natom
Exiting. All files have been retained.

which says the number of ligand+receptor doesn’t match the complex. I went
back and checked the number of atoms in the topology file, it is 9478
(receptor) , 712 (ligand) and 10190 (complex) which should match but
Is this because I ran the simulation with the wrong order initially? or it
is because I am missing something?
Thank you for your help

On Fri, Aug 5, 2016 at 7:49 PM, David A Case <> wrote:

> On Fri, Aug 05, 2016, maryam azimzadehirani wrote:
> > TrajError: Could not find number of frames in
> > mmgbsa_80_100_reimage_100f.mdcrd
> > I checked the trajectory and inputs and everything seems to be OK.
> Can you say exactly how you decided that everything was OK? First thing
> to do is to use cpptraj to open the file listed above, and find out how
> many frames it has. Be sure to use the same prmtop file as the mm/pbsa
> script is using.
> ...dac
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Received on Mon Aug 08 2016 - 00:30:02 PDT
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