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 - 10:30:04 PST
