My earlier mail got marked up. So, I am resending it.
I ran the script for 5 frames with trajout to pdb files as suggested. I got 5 pdb files. Each of them loaded normally in vmd without any streaks. The avg structure in the earlier run and in the present 5 frame run looked normal in vmd.
Jaya.
On 05/12/10, Thomas Cheatham III <tec3.utah.edu> wrote:
>
>
> > 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 - 13:30:09 PDT
