Hi,
I was using VMD to view the output. For the .trj with only CA, I used
a refh.pdb which only had .CA atoms. This was made by taking just the
CA atoms from the input structure file as I wanted to compute covar
w.r.t this initial structure.
Anyways, in debugging my problem I have simplified the script
(involving center to a particular region on the protein) to
following,(but this still doesn't works for all the frames. Some
frames are viewed fine but then the others are all garbled):
trajin 1.trj 1 10000 200
trajin 1b.trj 1 10000 200
trajin 1c.trj 1 10000 200
trajin 1d.trj 1 10000 200
trajin 1e.trj 1 10000 200
trajin 1f.trj 1 10000 200
trajin 1g.trj 1 10000 200
center :509-513
image origin center familiar
trajout out.trj
I viewed the trajectory with VMD by using initial .prmtop file as used
in the simulation.
Please suggest.
Thanks,
AJ
On Wed, Oct 6, 2010 at 6:43 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>> 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.
>
> Another option would be to visualize all atoms, but hide the ones
> you don't want to see. Maybe VMD could do this?
>
> Bill
>
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Received on Wed Oct 06 2010 - 16:30:02 PDT
