On Thu, May 13, 2010, sunita gupta wrote:
>
> I am a new user of Amber and I have a query regarding adding restraints. I
> am trying to run thermodynamic Integration of Protein-ligand solvated in
> water box. I want to add distance restraints between protein and ligand in
> order to avoid movement of ligand from its active site. I don’t want to
> recompile Amber as after editing the *“map.DG-AMBER”* (as its not
> recognizing DRG) I will have to…
No recompiliation is needed after editing the map.DG-AMBER file.
>
> So, I thought of manually making DISANG file (as per mailing list
> recommendation for less no. of bonds).
>
> I am not sure if, I am placing the correct values in DISANG file…... Eg.
Looks fine to me. But these restraints are extremely strong (rk2=20.):
you won't sample enough of the real configuration space of ligand this way,
so it will probably be difficult to interpret any free energy estimates you
get.
Since you are a new user, be sure you are comfortable running standard
simulations (you need to do this anyway to prepare your system) before trying
advanced things like thermodynamic integration.
....good luck....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 13 2010 - 05:00:07 PDT
