problem of reading trr/top files

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Liang Li

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Dec 14, 2015, 1:09:49 AM12/14/15
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Hello,

I am new to MDAnalysis and trying to read topology and trajectory files from .top and .trr resulted from one of my simulations.
the file were read:


mol = MDAnalysis.Universe('filename.top', 'filename.trr')

error messages: xxx.top is not a valid TOP file. %VE Missing in header

if the TOP file was replaced by a TPR file, the problem resolved but for the trr file,

UserWarning: Aborted loading offsets from file; ctime or size did not match

-does this mean the failure of reading trr file?

what do these mean in your experience? Noting that these files are results from a validated simulation, should't exite any error in their file format or it wouldn't be run in gromacs.


thanks 

Liang


Oliver Beckstein

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Dec 14, 2015, 1:11:14 AM12/14/15
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Hi Liang,

Gromacs top files cannot be read. Use the tpr or a gro or a PDB. 

Best wishes,
Oliver

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Oliver Beckstein

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Max Linke

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Dec 14, 2015, 2:18:16 AM12/14/15
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On Monday, December 14, 2015 at 7:09:49 AM UTC+1, Liang Li wrote:
UserWarning: Aborted loading offsets from file; ctime or size did not match

No the trr file was read fine. To support efficient random seeking in trr files MDAnalysis
saves the offsets for each frame in a trr-file. When you reopen a trr we do some consistency
check to see if the saved offsets are still valid, if these checks fail we issue the UserWarning
and recalculate the offsets.

Liang Li

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Dec 14, 2015, 6:23:13 AM12/14/15
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well understood, much appreciation.

Liang

Liang Li

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Dec 14, 2015, 6:23:13 AM12/14/15
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Hi Oliver,

thanks for responding, I have replaced .top by a .tpr file, while loading a .trr file, get a warn message :
"Aborted loading offsets from file; ctime or size did not match."

Does this mean the trajectory file was errorly read?


Cordially

Liang


On Monday, December 14, 2015 at 2:11:14 PM UTC+8, Oliver Beckstein wrote:
Hi Liang,

Gromacs top files cannot be read. Use the tpr or a gro or a PDB. 

Best wishes,
Oliver

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Oliver Beckstein


Am Dec 13, 2015 um 22:53 schrieb Liang Li <liang....@gmail.com>:

Hello,

I am new to MDAnalysis and trying to read topology and trajectory files from .top and .trr resulted from one of my simulations.
the file were read:


mol = MDAnalysis.Universe('filename.top', 'filename.trr')

error messages: xxx.top is not a valid TOP file. %VE Missing in header

if the TOP file was replaced by a TPR file, the problem resolved but for the trr file,

UserWarning: Aborted loading offsets from file; ctime or size did not match

-does this mean the failure of reading trr file?

what do these mean in your experience? Noting that these files are results from a validated simulation, should't exite any error in their file format or it wouldn't be run in gromacs.


thanks 

Liang


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Oliver Beckstein

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Dec 14, 2015, 12:33:44 PM12/14/15
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That's not a problem. It just means that MDAnalysis recomputes trajectory frame indices. 


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