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? 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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