AMBER Archive (2007)

Subject: Re: AMBER: How to delete particular frame from mdcrd file (not with ptraj).

From: saurabh agrawal (imsam100_at_yahoo.co.in)
Date: Wed Aug 22 2007 - 05:25:53 CDT

Thanks Steve

I saw the trajectory it has thousands and thousands
values. May you please let me know the way to trace a
particular frame form full trajectry. eg. I need to
detete frame 668.
How it is possible.

thank you again.

saurabh

--- Steven Winfield <saw44_at_cam.ac.uk> wrote:

> Dear Saurabh,
>
> You could work out how many lines per frame there
> are in the mdcrd file
> then use 'head' to cut out the frames before the bad
> one, 'tail' to get
> those frames after the bad one, then 'cat' the two
> results into a new
> mdcrd file:
>
> $ head -n (lines/frame x frames before) mdcrd >
> before.mdcrd
> $ tail -n (lines/frame x frames after) mdcrd >
> after.mdcrd
> $ cat before.mdcrd after.mdcrd > new.mdcrd
>
> Steve.
>
> saurabh agrawal wrote:
> > Hello All,
> >
> > One frame of my mdcrd file is gone bad and not
> > readable with ptraj or VMD software.
> > I can see them through Chimera but since chimera
> do
> > not have the facility of deleting a particule
> frame
> > form whole trajectory, I am unable to do that.
> >
> > I need to delete that frame for rmsd generation
> and
> > other analysis through ptraj.
> >
> > Please let me know the possible ways for doing
> this.
> >
> > waiting for kind replys.
> >
> > saurabh
> >
> >
> > Download prohibited? No problem. CHAT from
> any browser, without download. Go to
> http://in.messenger.yahoo.com/webmessengerpromo.php/
> >
>
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