Hi Everyone,
Currently I’m simulating a protein-protein complex membrane system and need help to re-image the protein complex to avoid complex-complex interaction through the periodic system. Specifically, my protein complex looks like a ’T’ where the vertical portion is one protein and the horizontal top cross is another protein thus giving my system a long axis.
To maximize simulation speed, by minimizing excess waters and lipids the system’s X and Y axis are not equal, { 107.968 72.309063 123.507529 } , however my protein complex is rotating and now the horizontal portion of the T are within 6A of touching. While literature supports a potential interaction this is outside the scope of my study due to the placement of the initial complex (which may not allow for optimal dimerization).
Is there a way to re-image or rms fit the simulation, from an rst file, back to the initial coordinates? I’ve tried various combinations of rms, image and autoimage without success. Any input would be greatly appreciated.
Parker
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Received on Mon Dec 29 2014 - 17:00:02 PST
