On Mon, Jan 19, 2015, Hadeer ELHabashy wrote:
>
> I have ran a simulation on a protein in water box with iwrapped periodic
> boundary conditions . and I have extracted the pdb and I expected to see
> the water box is replicating itself around the protein however I found part
> of the protein is out of the water box and no surrounding water (attached
> screen shot by VMD). So, how can I see a periodic image of the protein in
> the water box .
Just use the autoimage command in cpptraj, which will recenter the waters
around your protein.
...good luck....dac
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Received on Sun Jan 18 2015 - 17:30:02 PST
