Re: [AMBER] RDF: corrupted trajectory

From: Daniel Roe <>
Date: Fri, 17 Jan 2020 13:47:57 -0500


This error could be innocuous, or it could be a problem. The issue is
that the ASCII trajectory format doesn't store how many atoms or
frames it has, so cpptraj tries to guess based on the expected
trajectory size (calculated from the number of atoms in the topology,
the size of the title, whether REMD lines are present etc). There can
be a few reasons why this fails:

1) Most common: you are providing a topology with a different number
of atoms than was used to generate the trajectory. Double check that
the topology used in the simulation that generated the trajectory is
the one you are using. This can also happen if you e.g. load a
stripped trajectory with the original topology etc.
2) Somewhat common: your simulation crashed and the trajectory
contains an incomplete frame. In this case cpptraj will read all of
the "good" frames. If the corrupted frame is in the middle of the
trajectory somehow this is bad and will fail. You should run the
'check' command on this trajectory to make sure things look ok.
3) Uncommon: Somehow you got some extra bytes in the file, maybe an
extra newline at the end? This can happen if e.g. you opened up the
trajectory in a text editor and accidentally hit "enter" or something.

Note that all of these become a non-issue if you use the default
netcdf trajectory format.


On Fri, Jan 17, 2020 at 11:04 AM emanuele falbo
<> wrote:
> Dear users,
> I have used packmol to make a leap input file (the input packmol file is a
> pdb),
> and the dynamics seems going perfectly. When getting the RDF from the
> trajectory using cpptraj I get the following error from cpptraj:
> *"Warning: 04_Prod_2.mdcrd: Could not accurately predict # frames. This
> usuallyWarning: indicates a corrupted trajectory or
> trajectory/topologyWarning: mismatch. Will attempt to read 277 frames.*
> However, cpptraj terminates the RDF calculation without problems.
> I do not know whether this error could be ignored, and thus
> the RDF can be trustable, or not. Do you have any suggestion ?
> Cheers,
> Manuele
> --
> *Emanuele Falbo*
> PhD student
> Penfold group
> School of Natural and Environmental Sciences
> Bedson Building, Newcastle University
> Newcastle upon Tyne, NE1 7RU
> w:
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> AMBER mailing list

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Received on Fri Jan 17 2020 - 11:00:02 PST
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