you can calculate the pairwise-decomposed energies (note that these are not
free energies, and also that they will not include solvation effects).
see the idecomp variable in the Amber manual.
On Mon, May 24, 2021 at 1:16 PM Rana Rehan Khalid <ray.binm.gmail.com>
wrote:
> Dear Amber Users
>
> I modified some already known inhibitors, Now I want to calculate binding
> free energy of each residue with respect to inhibitor, But I do not want
> the surrounding residues to contribute to the energy of a particular
> residue which is interacting with the ligand. As I know, we can perform
> per-residue decomposition analysis in amber but in this analysis we can get
> each residue decomposition energy but this energy also has the contribution
> of surrounding residue. Please correct me if i am wrong. Also guide me how
> I can calculate energy contribution of a particular residue towards ligand
> without considering surrounding residue impact on that particular residue.
>
> Looking forward to hearing from you.
> Best wishes
> Rehan
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 24 2021 - 10:30:03 PDT
