[AMBER] Bad Frames in Corrupted Trajectories

From: Amanda Li <aml016.ucsd.edu>
Date: Wed, 3 Jun 2015 12:22:55 -0700


I have generated trajectory files that seem to have been corrupted, most
probably by an I/O issue. They are in NetCDF format, and when I try to
process them using cpptraj, I see the following error for certain frames:
"Warning: Frame XXXX coords 1 & 2 overlap at origin; may be corrupt."
Indeed, when I do go to frame XXXX by looking at the trajectory in a
visualizer or using ncdump, something is clearly amiss at that frame, but
most of the trajectory is still fine. My mdout files also look free of

I have two questions regarding handling these bad frames:
(1) *What is the most efficient way out counting out these bad frames?*
Should I just load them into cpptraj and count the number of warnings I am

(2) *Why do my action commands still process the bad frames even when I put
"check <mask> skipbadframes silent" before them?*
If I give cpptraj these lines:

check <mask> skipbadframes silent

distance d1 <mask1> <mask2> out tmp.dat

I expect tmp.dat to not contain the bad frames, but this is not the case.
The output includes these frames and gives them a distance of 0.0. Is this
the correct behavior? Is there a way to request that the bad frames be
excluded from the output file?

Thank you!

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Received on Wed Jun 03 2015 - 13:00:02 PDT
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