Re: [AMBER] Problem with CPPTRAJ (RMSD)

From: Daniel Roe <>
Date: Tue, 3 Sep 2019 08:38:40 -0400


First, could you say what version of cpptraj you are using?

On Tue, Sep 3, 2019 at 1:22 AM Rui Chen <> wrote:
> I have 1000 frames in the dcd file, maybe because it's not AMBER format,
> CPPTRAJ only read 123 frames. What should I do? Maybe I need to convert dcd
> into AMBER format? How to do that?

Are you certain you have 1000 frames? Cpptraj checks the number of
frames in Charmm (DCD) trajectories in two ways. First it reads what
is written in the header. However, because this number is not always
accurate it then checks the file size based on the expected number of
frames. If the size does not match (because e.g. the MD run crashed or
something) cpptraj will print out a warning. Can you post your entire
cpptraj output?

> 2.
> [image: Screen Shot 2019-09-02 at 11.11.11 PM.png]
> Is the second warning about unit cell a big deal? How can I correct it?

This warning is just FYI and means exactly what it says - don't try
any imaging routines after you do the RMS fit. This warning was added
because every once in a while users would do imaging after RMS-fitting
and end up with a garbled system.


> Looking forward to hearing from you.
> Best regards,
> Rui
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Received on Tue Sep 03 2019 - 06:00:03 PDT
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