On Mon, Feb 22, 2016, Dan Morris wrote:
>
> This is my first message to the AMBER list, sorry if I am doing it wrong.
Although SHIFTS uses AmberTools, it is not really a part of Amber. Better
to send problem reports directly to me.
>
> I am trying to use SHIFTS 5.0.1 to calculate theoretical proton shifts in a
> protein structure. I have found success with apo simulations, however
> SHIFTS will not recognize ligand molecules in my input PDB files and
> removes them to a separate nonprot.pdb file before performing calculations
> on the apo structure.
>
> Any advice would be greatly appreciated. To put this into perspective
> I have a database of ligand pose coordinates all bound to the apo
> structure of my protein. I'm trying to compare simulated chemical
> shift perturbation to experimental shifts so I can computationally
> filter the poses.
Do you want to see the effect of the ligand on the shifts in the protein?
Or to see how the shifts in the ligand change as a function of binding pose?
(Or both)?
What you are trying to do is not a standard SHIFTS operation, and the sorts of
things you need to do depend on which SHFITS it is you want to compute. If
you are willing/able to send me one snapshot PDB file, I'll try to help with
getting things going.
...dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Feb 23 2016 - 05:30:03 PST
