On Wed, Oct 6, 2010 at 2:45 PM, Ajay Ummat <ajayummat.gmail.com> wrote:
> When I try to run ptraj with the following script, I don't get any
> meaningful trajectory (instead its bunch of lines all over the place):
Bill is right; if your output format is an Amber trajectory, you need
a corresponding Amber topology file in order to view it correctly. I'm
not sure if it's currently possible to generate a topology with only
CA atoms, but this is what you would need.
If you really need to visualize this I think the only option (although
certainly not very practical or convenient considering the number of
frames you are generating) would be to output the structures as PDB
files.
> How can I image the drifted DNA strand
> back into the structure. I have used image origin center familiar in
> Ptraj and can't get it to work. When I couple this command with
> multiple trajin's again all I get is a bad output .trj file. Not sure
> where things are getting weird.
In my experience with DNA centering on the first strand, imaging, then
centering on both strands and imaging again works. This should be done
separate from any RMS fitting since that will change around the
coords.
-Dan
>
> Thanks in advance.
>
> Best, AJ
>
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Received on Wed Oct 06 2010 - 15:30:04 PDT
