> > All of this sounds very strange to me. Does your average structure calculated on
> > the compound trajectory you made with nobox look "normal"?
>
> I checked this structure and found that it is not correct. So I think that
> there is something wrong witht he compound mdcrd file created but what it
> is I dont know.
....
> I checked the individual mdcrd files and generated the average structure
> using each one separately. I found that that the structures thus generated
> are perfectly all right. Also I generated pdb structures for all the
> frames from individual mdcrd files. and these structures are also all
> correct.
>
> I also tried to generate the pdb structures and average structure from the
> individual mdcrd files using the nobox keyword and these structures were
> exactly the same as that generated without the use of nobox.
If I understand your problem correctly, you see garbage results when you
go back and re-do the analysis using the trajectory file created by ptraj
that is the aggregate of the separate trajectories. This is a bit
confusing.
When you created the "aggregate" trajectory with the commands:
ptraj mod9.prmtop << EOF
trajin gbmd-pr.mdcrd
trajin gbmd-pr-1.mdcrd
trajin gbmd-pr-2.mdcrd
trajin gbmd-pr-3.mdcrd
trajin gbmd-pr-4.mdcrd
trajin gbmd-pr5.mdcrd
trajout grp3.mdcrd
The output trajectory (grp3.mdcrd) will, I believe, add box information
(stupidly) even though box information is not present (which I assume is
the case since you named the input trajectories as gbmd*).
If you change the trajout to
trajout grp3.mdcrd nobox
This, as Kristina mentioned, should create a valid trajectory (assuming
you aren't doing anything else inside like shifting the coordinates, etc.)
that will be properly processed using the same prmtop (mod9.prmtop).
Otherwise I am a bit confused as well...
[Note, this is why this trajectory format is particularly poor since there
is no way to easily detect corrupt frames, correspondence to a given
prmtop, etc.]
Let me know if I can be any more help.
--tom
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Received on Wed Feb 02 2005 - 18:53:00 PST
