Hi Dan & Carlos,
I apologize. I was confused as I know that my trajectory file contains
245,755 frames, but it was showing just 1750 frames. But, apparently I was
trying to run a different file.
Thanks,
Catherine
On Mon, Feb 3, 2020 at 2:13 PM Daniel Roe <daniel.r.roe.gmail.com> wrote:
> This message was sent from a non-IU address. Please exercise caution when
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> -------
>
> Hi,
>
> On Mon, Feb 3, 2020 at 1:13 PM Catherine Jenifer Rajam Rajendran
> <catrajen.iu.edu> wrote:
> > * When I read my MDCRD file in CPPTRAJ, it shows that it's reading 18 of
> > 1750 frames.
> >
> > INPUT TRAJECTORIES:
> > 0: 'prod_noW.mdcrd' is an AMBER trajectory, Parm native_nowat.top
> (reading
> > 18 of 1750)
> > Coordinate processing will occur on 18 frames.
> >
> > My mdcrd file actually contains 245,755 frames as per the following
> email:
> > http://archive.ambermd.org/201107/0414.html
>
> Are you sure you did your math correctly here? Cpptraj bases the #
> frames calculation for ASCII trajectories on the number of atoms in
> the associated topology and the actual file size. The calculation
> rarely fails if the topology and trajectory match.
>
> >
> > * When I TRAJIN my mdcrd file, I got the following warning:
> >
> > Warning: Trajectory only contains box lengths and topology has no box
> info.
> > Warning: To set box angles for topology use the 'parmbox' command.
>
> This is likely because the trajectory was stripped but 'nobox' was not
> used, so the trajectory still contains box coordinates.
>
> >
> > So, apparently my topology file doesn't have box information but my
> > trajectory file has box coordinates. Should I skip reading the box values
> > from trajectory file? If so, Can can I do it. And, I would like to know
> if
> > there is a way to understand why it reads less number of frames. Can
> > someone help me with this?
>
> Your trajectory contains 1750 frames. Since according to the output
> you posted you're only reading in every 100th frame, you end up
> reading only 18 frames.
>
> -Dan
>
> >
> > Thanks,
> > Catherine
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Received on Mon Feb 03 2020 - 12:00:02 PST
