> After putting the trajout statement after the strip command, I do not
> see the box shape. The number of frames are also consistent with 2400
> frames. But the atoms are still streaking in the vmd display. I am
> attaching a picture of the image as jpg file. Jaya.
The position of the trajout, in all versions of ptraj, is irrelevant.
What is likely true is that there is a mismatch between your trajectory
and your loaded prmtop (as mentioned by Prof. Simmerling). (By the
way, from the scripts shown previously you loaded AMBER trajectory format
files, not binpos).
The offsets seen in your movie are consistent with the AMBER trajectory
not having box information, but the prmtop having box information (or
vise-versa). In this case, usually the first frame (in a VMD movie) looks
OK, and subsequent ones get shifted.
To verify things are OK and its a prmtop mismatch, do your script the same
for ~5 frames...
trajin mdcrd 1 5 1
and change the trajout to PDB files and look at these.
trajout tmp-pdb pdb
(or also look at your avg.pdb)
--tec3
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Received on Wed May 12 2010 - 13:30:04 PDT
