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 - 10:30:02 PDT
