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: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Wed May 16 2007 - 06:09:01 CDT

it might help if you incldue the entire ptraj input and then the error,
rather than telling us part of it. I can't really follow what you are
saying.

did you try what Gustavo suggested :

trajin mdcrd 92 92 1

On 5/16/07, j j <fantvamp_at_gmail.com> wrote:
>
> Thank you for your answer.
> Yes I've tried it, that is:
> #10-trajin filename [ start stop offset ]
> But in a trajectory splitted in several files i would like
> to load the starting xyz file (initial state before md, restart format)
> and the collected frames in each coord file (trajectory of
> 20 frames each). When ptraj load all the states you can see
> while processing, a dot for each frame, or a space if you
> stablish a start frame or offset. At the end ptraj tells you how
> many states do you have. I think ptraj first load all the
> instructions and after start proccesing. Maybe I
> was not having into account something similar to
> the trajin in the trajout that is:
> For example in <Successfully read in 441 sets>
> If I just specify frame as start 92:
> WARNING in ptraj(): trajectory start is > stop; no
> configurations will be processed
> AMBER trajectory (with box info) with 20 sets (processing only -71)
> ...
> I have a total of 441 but i have been collecting 20 in each coord
> If I specify 92 in the xyz and after 92 92 in the coords:
>
> 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
> Successfully read in 441 sets and processed 0 sets.
> ...
>
> If I specify 92 92 92 then:
> 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
> WARNING in ptraj(): Offset is so large that only 1 set
> will be processed...
>
> ptraj has got the ability of auto recognice the format of inputs,
> thus giving you the possibility of load combined files (pdb, restart,
> trajectory..)
> maybe I was not having into account sth like
> trajout filename [ start stop offset ]
> I apologize for the mess,
> 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.
> >
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>
>
>
> --
> fantvamp

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