Re: [AMBER] [External] Re: Reading Frames from Trajectory File

From: Catherine Jenifer Rajam Rajendran <catrajen.iu.edu>
Date: Mon, 3 Feb 2020 14:03:48 -0500

Hi Carlos, I am trying to skip every 100 frames.

On Mon, Feb 3, 2020 at 1:56 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:

> 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
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>


_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber


Received on Mon Feb 03 2020 - 11:30:02 PST
Custom Search