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.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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Received on Sun May 20 2007 - 06:07:04 PDT
