md analysis query

[Viswanath Vittaladevaram]

Hi,

I am trying to use this command below

python traj_residue-z.py -g fnIII-12_SAMch3_T298_0.gro -x fnIII-12_SAMch3_T298_pbc.xtc -o1 fnIII-12_SAMch3.protein-z -o2 fnIII-12_SAMch3.res-z --nres 92

I got this error! could you help on this,thanks

/opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/MDAnalysis/coordinates/XDR.py:196: UserWarning: Reload offsets from trajecto

 ctime or size or n_atoms did not match

  warnings.warn("Reload offsets from trajectory\n "

Traceback (most recent call last):

  File "traj_residue-z.py", line 32, in <module>

    u=MDAnalysis.Universe(groFile,xtcFile)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/MDAnalysis/core/universe.py", line 337, in __init__

    self.load_new(coordinatefile, **kwargs)

  File "/opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/MDAnalysis/core/universe.py", line 613, in load_new

    trj_n_atoms=self.trajectory.n_atoms))

ValueError: The topology and XTC trajectory files don't have the same number of atoms!

Topology number of atoms 47333

Trajectory: fnIII-12_SAMch3_T298_pbc.xtc Number of atoms 1416

[Lily Wang]

Hi Viswanath,

It looks like you’ve post-processed your XTC file to strip out some atoms, e.g. the solvent. The XTC file has 1416 atoms but the GRO file has 47333 atoms. While I don’t know what’s in your script, it looks like you need to either:

• Use a XTC file with all the atoms, or
• Process your GRO file to strip out the same atoms as in the XTC

Hope that helps.

Cheers,

Lily

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[Viswanath Vittaladevaram]

Hi,

Thanks for your reply. Did you mean instead pbc.xtc , should I need to use .xtc file in command line?

Regards,

Viswanath.V

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[Lily Wang]

Hi Viswanath,

Quite possibly, if you stripped atoms out in pbc.xtc. However, you would be the best person to know what to do here, as we don’t know what is in your XTC files. If you use gmx check -f my_xtc_file.xtc, you can check how many atoms are in them.

Cheers,

Lily

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[Viswanath Vittaladevaram]

Hi.

I checked with .xtc file and it is matching with gro file. Then I changed the command line and it worked.

Thanks,

Viswnanath.V

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[Viswanath Vittaladevaram]

python traj_cv.py -g fnIII-12_SAMch3_T298_0.gro -x fnIII-12_SAMch3_T298_pbc.xtc -o1 fnIII-12_SAMch3.protein-z -o2 fnIII-12_SAMch3.res-z --nres 92

I got this error! could you help on this

/opt/local/Library/Frameworks/Python.framework/Versions/3.7/lib/python3.7/site-packages/MDAnalysis/coordinates/XDR.py:196: UserWarning: Reload offsets from trajecto

 ctime or size or n_atoms did not match

  warnings.warn("Reload offsets from trajectory\n "

Earlier I did using other python file and it showed some error and was able to load again showing same number of atoms for gro and xtc files. But this time error is just showing as mentioned above and I don't see further!

[Oliver Beckstein]

Hi Viswanath,

If you only saw the “Reload offsets” warning and everything worked as expected then there is no problem. It just meant that MDAnalysis did not know what was in your XTC file (maybe it was moved or renamed) and it had to read it again and build the index of all frames. (The offset files are explained in the note for XDRReaders https://docs.mdanalysis.org/stable/documentation_pages/coordinates/XDR.html#MDAnalysis.coordinates.XDR.XDRBaseReader). 

Rebuilding the offset file takes time so if this happens regularly then you should try to figure out what happens to your offset file (a hidden file ending in _offsets.npz) and your trajectory. One possible problem occurs if the directory in which the XTC resides is not writable. Then the offsets are only created in memory and the next time you run your script, the offsets have to be rebuild again, instead of being read from the offset file.

Oliver

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[Viswanath Vittaladevaram]

Hi,

Thanks for your reply. 

Earlier I tried running the command and it worked but the format of the file was in xtc.

But this time the file format is in trr.

Is it due to this reason?

With regards,

Viswanath.V

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[Viswanath Vittaladevaram]

Hi,

Residue number at the end of command was modified and it worked.

Thanks,

Viswanath.V

On Thu, Jun 16, 2022 at 12:14 AM Oliver Beckstein <orbe...@mdanalysis.org> wrote:

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