On Thu, Oct 27, 2011 at 1:46 AM, Mo Chen <mc842.cornell.edu> wrote:
> On Thu, Oct 27, 2011 at 1:24 AM, Mo Chen <mc842.cornell.edu> wrote:
>
> Hi Jason,
> Now I reconsider it and think that restraining the force direction is
> probably not a good idea in this case because it limits the ligand
> behavior.
> Though it might be nice if Amber does have this option. Thank you!
>
> Best,
> Mo
>
>
SMD only works by defining a reaction coordinate. If you want to pull a
ligand out of a protein in a certain direction, you'll need to somehow
define a reaction coordinate that is unidirectional. For instance, you can
insert a dummy particle with no charge or VDW terms and restrain it to a
particular position relative to the protein (via NMR restraints), and define
a generalized distance constraint involving the distance between the active
site and ligand minus the distance between the ligand and the dummy
particle, and scan it from -20 angstroms (or whatever the starting value for
your system is) to 20 angstroms (or whatever the ending value would be).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Oct 27 2011 - 06:30:02 PDT
