Thank you for your early response.
Best
On Mon, May 24, 2021 at 1:21 PM Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 24 2021 - 10:30:03 PDT
