Re: [AMBER] [cpptraj] Nativecontacts failing with long trajectory

From: Daniel Roe <>
Date: Wed, 22 Jul 2015 14:53:18 -0600


What version of cpptraj are tou using? Also, can you provide your cpptraj
input and output? Thanks,


On Wednesday, July 22, 2015, Juan Eiros Zamora <> wrote:

> 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,
> Juan
> _______________________________________________
> AMBER mailing list
> <javascript:;>

Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
(801) 587-9652
(801) 585-6208 (Fax)
AMBER mailing list
Received on Wed Jul 22 2015 - 14:00:02 PDT
Custom Search