Interactions between compounds

User discussions
1

GROMACS version: 2023.3
GROMACS modification: No

I have a molecule with 3 functional groups which can interact with the target structure. Simply put, the structure is A-B-C where A and C are chemically equivalent functional groups while B is different.
The molecule can interact via any of the 3 functional groups involving one or more from amongst A, B and C so the possible scenarios are: only one functional group interacts (A, B or C), two groups interact simultaneously (AB, AC, BC) or all three groups interact simultaneously with the target structure.

Analysing the distance distribution of A, B and C individually using rdf analysis allows analysis of each of these groups individually. I was wondering if there is a way to look at if 1, 2 or 3 groups are interacting simultaneously?

Regards,
Raman

2

Can information be simply obtained from the center of mass (COM) distance between groups? Utilize the gmx distance tool to compute distances between atom or group pairs. When considering interactions, examining interaction fingerprints might be more insightful. Various web-based or Python tools are available to perform this analysis, serving as a complementary approach.