VMD-L Mailing List

From: Edward Lyman (edward.lyman_at_gmail.com)
Date: Fri Oct 31 2008 - 14:07:08 CDT

Dear all,

I am trying to think of a way to find a conformation of a linker, consisting
of 6 or so residues, that is consistent with the fixed orientation of two
domains on either side. Ideally I could fix the two domains and then run
some sort of MC or MD based optimization to get a reasonable starting
configuration for the linker. A less satisfactory way would be to rotate a
dihedral, and the rest of the domain along with it, and just look at it and
see if i like it.

Thnx,
Ed Lyman