Hello,
The version of cpptraj I am using is V17.00.
Best regards,
Rui
On Tue, Sep 3, 2019 at 6:39 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> First, could you say what version of cpptraj you are using?
>
> On Tue, Sep 3, 2019 at 1:22 AM Rui Chen <rchen6.ualberta.ca> 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.
>
> -Dan
>
> >
> > Looking forward to hearing from you.
> >
> > Best regards,
> > Rui
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Received on Tue Sep 03 2019 - 08:30:02 PDT
