Ligand atom selection around a particular distance around protein atoms

[akashp...@gmail.com]

Hi all,

I wanted to calculate the number of ligand N atoms around 6A of  protein heavy atoms as a function of simulation time (frame). Here is the code I have so far:

import MDAnalysis as mda

u = mda.Universe(top, traj)

protein = u.select_atoms("index 0:6614 and not name H*")

protein

<AtomGroup with 3336 atoms>

lig = u.select_atoms("index 6615:8154 and name N")

lig

<AtomGroup with 154 atoms>

for ts in u.trajectory:

      lig_6A = ("lig around 6 protein")

I get an error saying MDAnalysis does not recognise 'around' and that 'AtomGroup' object is not callable. Please advise  me on how I can extract the number of N atoms (ligand) around 6 of protein heavy atoms as function of time?

Best wishes,

Akash