[AMBER] [cpptraj] Nativecontacts failing with long trajectory

From: Juan Eiros Zamora <j.eiros-zamora14.imperial.ac.uk>
Date: Wed, 22 Jul 2015 20:36:08 +0100

Hi everyone,

I've got a large trajectory file obtained from different independent
runs and I want to use the nativecontacts command to analyze it.

I have 4 nativecontacts analysis to do, which work fine if I use a
subset of the data. But if I load the whole thing, the contact residue
pairs files come up incomplete (some have only a subset of the pairs,
and the last one only has the header). All those files are written
properly if I use a small set of the data, so I'm guessing it's not a
problem of the analysis per se.

How can I figure out the offset I have to use when loading the big
trajectory to minimise accuracy loss on the analysis? That's the only
alternative that comes to mind, but I would like to use all the frames
(even if it takes awhile) if that's possible.

Thanks in advance for any suggestion,

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Received on Wed Jul 22 2015 - 13:00:03 PDT
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