[gmx-users] Interaction study for peptide-receptor..

[rama david]

Hi gromacs Friends,
            I want to do peptide-receptor ( Protein) interaction
study.Receptor consist a single chain.
Peptide is made up  of  4 amino acids. I know the interaction pattern of
peptide and receptor.
I plan to mutate single residue each at a time and  run 4 simulation .
So I will have the 4 different simulation that contain the mutated residues
and the wild one.


Then afterward from the interaction energy I want to select the peptide
which is showing
stronger interaction than others.

As  mention I know the binding site, If I freeze the remaining portion in
receptor
that not involved in binding , Is it going to affect my screening process
???

Or there is any other way to do these process???


thank you in Advance

With Best wishes and regards,
Rama david