Hi,
You could just do 2 extra energy calculations and subtract them out:
energy Eligand :164
energy Ereceptor :1-163
energy Etotal :1-164
run
Einteraction = Etotal - Ereceptor - Eligand
writedata Einteraction.dat Einteraction
Hope this helps,
-Dan
On Thu, Apr 29, 2021 at 2:01 PM German P. Barletta <pbarletta.gmail.com> wrote:
>
> Dear amber users and developers,
>
> I'd like to calculate the nonbonded (LJ + Coulombic) energy terms for the
> interaction between a ligand (residue 164) and a protein (residues 1-163)
> but if I use the mask ":1-164", cpptraj will also include the interactions
> of the protein and the ligand with themselves.
>
> gromacs tutorials
> <http://www.mdtutorials.com/gmx/complex/09_analysis.html> show
> a convenient way to do this, but how can I do the same with cpptraj?
>
> Thanks!
> _______________________________________________
> 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 Fri Apr 30 2021 - 09:00:03 PDT
