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<TITLE>solvent within 3.5 angstrom of protein.</TITLE>
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<P><FONT SIZE=2>Hi,<BR>
<BR>
Im attempting to get all solvent within 3.5 angstrom of the protein and not doing well so far.<BR>
<BR>
This is for a system using dodecahedral periodic boundary conditions.<BR>
<BR>
Ive tried the various -pbc options on trjconv - in particular cluster but I dont think this has worked - there are protein residues<BR>
close to the dodecahedron surface which I think should have periodic image related waters closer.<BR>
<BR>
Is there another program I should be using?<BR>
<BR>
My protein from the raw coordinates is mostly outside the water cube so some form of transformation is needed.<BR>
<BR>
Thanks<BR>
<BR>
David<BR>
<BR>
PS this is probably html email sorry - Im having to use crappy webmail because of anti-spam issues with my sending<BR>
to these lists which so for seem to have been mostly rejected silently.</FONT>
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