On Mon, Oct 12, 2009, Jayalakshmi Sridhar wrote:
>
> I would like to do MD simulations on a receptor protein- it has
> extracellular region, transmembrane region and intracellular region. Is it
> possible to carry out MD simulation of the entire protein with parts of the
> protein in different solvent boxes. How can I specify a particular solvent
> box for one part of the protein and a different solvent box for the next
> part of the protein?
As Bill Ross pointed out, you don't really have different "boxes". The
Schulten group has some nice tutorials on simulations of membrane proteins +
membranes + water:
http://www.ks.uiuc.edu/Training/Tutorials/
...good luck...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 12 2009 - 15:00:03 PDT
