Dear Dan,
Thank you for your reply. I will have a try.
Best regards,
Rui
On Tue, Sep 3, 2019 at 11:06 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> In general, I recommend you use the latest version of cpptraj, either
> from AmberTools 19 or better yet, GitHub
> (https://github.com/Amber-MD/cpptraj).
>
> You should definitely make certain you actually have 1000 frames in
> your DCD trajectory. Cpptraj will print out the number of header bytes
> etc which you can use to check this if you do 'trajin' with the debug
> level set to 1 or higher, e.g.
>
> debug trajin 1
> trajin mytraj.dcd
>
> -Dan
>
> On Tue, Sep 3, 2019 at 11:19 AM Rui Chen <rchen6.ualberta.ca> wrote:
> >
> > 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 - 10:30:03 PDT
