Can you include your entire cpptraj script?
On Mon, Feb 3, 2020, 1:51 PM Catherine Jenifer Rajam Rajendran <
catrajen.iu.edu> wrote:
> Hi Carlos,
>
> Yes, I checked. The number of atoms are the same in both files. Both
> doesn't have water.
>
> Thanks,
> Catherine
>
> On Mon, Feb 3, 2020 at 1:26 PM Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > This message was sent from a non-IU address. Please exercise caution when
> > clicking links or opening attachments from external sources.
> > -------
> >
> > are you certain that your prmtop and your trajectory match in terms of
> > number of atoms? if you removed water from the trajectory, are you using
> a
> > prmtop that also has no water?
> >
> > On Mon, Feb 3, 2020 at 1:13 PM Catherine Jenifer Rajam Rajendran <
> > catrajen.iu.edu> wrote:
> >
> > > Dear Amber Users,
> > >
> > > * 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
> > >
> > > * 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.
> > >
> > > 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?
> > >
> > > Thanks,
> > > Catherine
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Received on Mon Feb 03 2020 - 11:00:03 PST
