From: Peter Murphy (pwmurphy_at_dal.ca)
Date: Mon May 13 2013 - 11:16:20 CDT
I have been playing around with the water_sphere.tcl script in the NAMD
tutorial, and have managed to get a larger water sphere, but the protein
I am attempting to solvate is not centered in the sphere. A Zip file
with the input/output PDB/PSF (V.H.-rACP/V.H.-rACP_ws_test) and tcl
script (original and my edited version water_rACP/water_rACP_test) can
be found at:
https://dl.dropboxusercontent.com/u/4078860/WaterSphere.zip
Thanks for any help you can provide,
Peter
-- Ph.D. Candidate, Dalhousie University, Halifax, NS Canada On 08/05/2013 9:06 AM, Peter Murphy wrote: > Hello Everyone, > > I am trying to increase the final size of the water sphere added > to a protein by wat_sphere.tcl. I have figured out how to increase the > initial water solvation box that is added, but can't figure out how > exactly to modify the deletion of water molecules such that a larger > sphere is left. > > Any help would be greatly appreciated, > > Peter > > -- > Ph.D. Candidate, > Dalhousie University, > Halifax, NS > Canada
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