VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Fri Oct 31 2008 - 14:37:34 CDT

Hi Ed,
modeller (http://www.salilab.org/modeller/) is pretty good at finding
reasonable loop conformations given a known loop sequence and a pair of
endpoints, so long as the loop is short. Their tutorials should have
some useful examples; you can do various types of force field-based
optimization.
Best,
Peter

Edward Lyman wrote:
> 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
>