Re: [AMBER] Bad Frames in Corrupted Trajectories

From: Daniel Roe <>
Date: Wed, 3 Jun 2015 13:40:59 -0600


On Wednesday, June 3, 2015, Amanda Li <> wrote:
> 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
> getting?

You can count the number of warnings (use 'noprogress' command to make this
easier) or create an output trajectory containing only 'good' frames via
'check skipbadframes'; then number of bad frames = frames in original traj
minus frames in new traj.

> (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?

They actually don't get processed, but because the frame number still
increases the bad frames essentially get placeholder values. This will be
true for any time series data set, but for other set types like a
coordinate covariance matrix etc, skipped frames are not included in the
calculation. Your best bet is probably to make a 'good' version of the
trajectory as mentioned above and then use that for processing.

Hope this helps,


> Thank you!
> ~Amanda
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Received on Wed Jun 03 2015 - 13:00:03 PDT
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