AMBER Archive (2007)

Subject: Re: AMBER: Is there any way to extract one frame from a whole trajectory just saving one file by using ptraj

From: j j (fantvamp_at_gmail.com)
Date: Wed May 16 2007 - 06:39:48 CDT

Thank you,
I'll append the whole trajectory in a big one or just
use the corresponding coord file instead of a list,
and then
trajin 12 12
trajout restart92 restart
instead of:
trajin list (441frames)
operations
trajout restart92 restart
sorry for the mess.
JJ

2007/5/16, Carlos Simmerling <carlos.simmerling_at_gmail.com>:
>
> well if you only have 20 frames in the trajectory then you can't read
> frame 92.
> it sounds like you are having trouble understanding what is in your files
> more
> than how to use ptraj. maybe you should first use ptraj to combine all of
> the frames to a single trajectory, then extract what you want. or, if you
> want
> #92 overall, and they are 20 per file, then 92 = 20 + 20 + 20 + 20 + 12
> so take frame #12 from file #5.
>
>
> On 5/16/07, j j <fantvamp_at_gmail.com> wrote:
> >
> > Sorry, you told me 92 92 1:
> > 92 92 1
> > FYI ptraj(): trajin stop value (92) is greater than the number of sets
> > read in
> > FYI ptraj(): Setting stop to the maximum value (20)
> > WARNING in ptraj(): trajectory start is > stop; no
> > configurations will be processed
> > Thanks,
> > JJ
> >
> >
> > 2007/5/15, Gustavo Seabra <gustavo.seabra_at_gmail.com>:
> > >
> > > j j wrote:
> > > > Dear amber users,
> > > > I'm using ptraj and I would like to extract a restart file from a
> > > > trajectory.
> > > > I know is the frame 92, so one way is going to the corresponding
> > > > trajectory file of the molecular dynamics by dividing the
> > > > number of frames collected in each trajectory file (20) and giving
> > > > as input just it.
> > > > But for example if I would like to process the whole trajectory
> > > > (Coordinate processing will occur on 441 frames),
> > > > Is there anyway to specify to ptraj that I want just to extract
> > > > the frame 92 after read all the frames without having to save
> > > > anything else?,
> > > > Thank you,
> > > > JJ
> > > >
> > > Have you tried to play with the 'trajin' options? My guess is
> > > something like
> > >
> > > trajin <file> 92 92 1
> > >
> > > should work, if you already *know* that the only one you want is frame
> > > 92. (I'm not sure if you would use 92 or 91 there though.)
> > >
> > > Gustavo.
> > >
> > > -----------------------------------------------------------------------
> > >
> > > The AMBER Mail Reflector
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> >
> >
> >
> > --
> > fantvamp
> >
>
>
> 

-- 
fantvamp

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