[EMAIL PROTECTED] 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.
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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