GROMACS version: 2020
GROMACS modification: Yes
I’ve seen examples where the number of contacts between a ligand and enzyme is determined. Is this calculated with or without hydrogens typically? I’ve seen examples where the average # of contacts per ligand heavy atom is quoted, which implies without. I was curious if anyone here knows which is more common (if one is)
Thanks in advance
I would never use hydrogens for this kind of calculation. Experimentally difficult to determine and it basically just inflates the number of contacts (is a CH3 really going to contribute 4 contacts to the count when it would suffice to use the C atom only?).
I agree. Do you use the -group option?
I have a pair of drugs that are identical other than one has a benzene ring and one is anthracene, both binding to the same residue (arginine). My understanding is that -group would count interactions between said arginine and benzene/arginine and anthracene as 1, whereas without -group, anthracene has more heavy atoms for potential contacts etc.
Again, it could just superfluously inflate the number of contacts. I suppose you could argue that not using -group would demonstrate the difference between the two moieties better than -group would.
Thank you for your advice as always
I don’t see why one would want to in most cases. If you want the number of contacts between two groups, simply constructing appropriate index groups (without H atoms) and choosing them both when prompted from
gmx mindist -on should do the job.
I am new in your community and not sure how to connect with the appropriate group!
Hence, here is my question:
Which command would calculate the number of contacts between two identical proteins (homodimer), more specifically “per residue”?
You need to set up appropriate index groups to do that, in concert with
gmx mindist -on. No command decomposes this quantity per residue, you’d have to make individual index groups, one for each residue of interest, and perform the analysis.