Re: [AMBER] GIST calculation on OpenMM trajectory

From: Franz Waibl via AMBER <>
Date: Thu, 23 Jun 2022 17:00:50 +0200

Dear Daniella,

is this problem still existing? I did not receive Mails from the Mailing
list for a while, probably due to a Spam filter.

Generally, gist should be able to work with other trajectory formats,
but I don't think it has been tested much. I would expect that the
topology format is more critical than the trajectory.

If the problem persists with the newest cpptraj version, you might want
to submit an issue on GitHub. You can also send me an example
trajectory+topology, and I will try to find the problem.

Best regards,


On 5/5/22 15:47, Daniella Hares wrote:
> Dear all,
> I would like to run GIST on a trajectory that was generated using OpenMM (.dcd format). Cpptraj is able to read in the dcd file but when I try to run the gist command it gives a segmentation fault (both AmberTools21).
> I've only found one similar thread in the mailing list archive from 2018 ( where gist did not work on NAMD generated trajectory. The original user solved the problem by using a different program (SSTMap).
> Has anyone been able to run gist on a trajectory that was not generated in amber?
> Any help is appreciated.
> Best wishes,
> Daniella
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Received on Thu Aug 04 2022 - 13:33:06 PDT
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