[gmx-users] solvent within 3.5 angstrom of protein.

[David van der Spoel]

David.Osguthorpe at UCHSC.edu wrote:
> 
> 
> Hi,
> 
> Im attempting to get all solvent within  3.5 angstrom of the protein and 
> not doing well so far.
> 
> This is for a system using dodecahedral periodic boundary conditions.
> 
> Ive tried the various -pbc options on trjconv - in particular cluster 
> but I dont think this has worked - there are protein residues
> close to the dodecahedron surface which I think should have periodic 
> image related waters closer.
> 
> Is there another program I should be using?

trjorder

> 
> My protein from the raw coordinates is mostly outside the water cube so 
> some form of transformation is needed.
> 
> Thanks
> 
> David
> 
> PS this is probably html email sorry - Im having to use crappy webmail 
> because of anti-spam issues with my sending
> to these lists which so for seem to have been mostly rejected silently.
> 
> 
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-- 
David van der Spoel, Ph.D.
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se