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

David.Osguthorpe at UCHSC.edu David.Osguthorpe at UCHSC.edu
Tue Jan 22 20:51:39 CET 2008


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?

My protein from the raw coordinates is mostly outside the water cube so some form of transformation is needed.



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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