From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Jan 21 2013 - 03:42:54 CST
I am observing a curious behavior in adding the solvation box, and
subsequent addions, with a heme protein. That is, to the dispdev
generated psf/pdb, add solvation (TIP3) produces a much elongated box
(X=102, y=63, z=75), from one side where there is nothing special
about this nearly spherical protein. Subsequent add ions (Na+, to
neutrality) places some Na+ in the elongated area, far away from the
As I said, all files in /parts, used for dispdev, are clean, free from
anything that would require solvation (and neutralization).
I understand that without seeing it is difficult to grasp what is
peculiar there. Perhaps similar affairs have already been noticed.
This archive was generated by hypermail 2.1.6 : Wed Dec 31 2014 - 23:20:52 CST