Hi SEB,
The lipids aggregated and surround the protein (as expected) but
asymetricaly in the box.
What do you mean with this? Did you consider PBC? Try centering your
system using the protein for the center of mass.
I have selected only the lipids from the last run
at a maximum distance of 20 A from the protein.
my problem is that my system is now circular (due to the lipid selection
method) and I want to put it in a new box
without adding more lipid or water but there will be no lipids in the
box corners.
Is there an easy way to solve this (the is no circular boxes and I have
some problems using dodecahedron ones)?
You could define a hexagonal prism, which is as close as you can get
to a cylinder.
Hope it helps,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623
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