Tutorial-l Mailing List

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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