error in setting up my Hydrogen Bond analysis (A beginner)

[naih222]

hi,
I am new to MD Simulation, as a way of practice I am trying to run a hbond analysis but I keep getting errors. I have 2 attempts with different error messages. Can someone help me sort this out?

import numpy as np
import MDAnalysis as mda
from MDAnalysis.analysis.hydrogenbonds import HydrogenBondAnalysis

ATTEMPT 1
THE ERROR IS "NoDataError: This Universe does not contain charge information"

THE CODE IS

Load the protein structure file and trajectory

psf = 'sol5.gro'
trajectory = 'traj_comp.xtc'

Create the MDAnalysis Universe

u = mda.Universe(psf, trajectory)

Define donor and acceptor selections

donors = "protein and name N" # Example: Nitrogen atoms in protein backbone
acceptors = "protein and name O" # Example: Oxygen atoms in protein backbone

Create HydrogenBondAnalysis object

hba = HydrogenBondAnalysis(u, donors, acceptors)

Run the analysis over the trajectory

hba.run()

Get the results

hbonds = hba.count_by_time()

Print the results

print("Time (ps) No. of Hydrogen Bonds")
for time, count in hbonds:
print(f"{time:.2f} {count}")

ATTEMPT 2
THE ERROR IS "AttributeError: 'HydrogenBondAnalysis' object has no attribute 'timeseries'"

import numpy as np
import MDAnalysis
from MDAnalysis.analysis.hydrogenbonds import HydrogenBondAnalysis

Load the protein structure file and trajectory

psf = 'sol5.gro'
trajectory = 'traj_comp.xtc'

Create the MDAnalysis Universe

u = mda.Universe(psf, trajectory)

Define the donor and acceptor groups

donors="name O"
acceptors = "name OH2"
hydrogens_sel="name H1 H2"

Perform the hydrogen bond analysis

hb = HydrogenBondAnalysis(u, donors, hydrogens_sel, acceptors, d_a_cutoff=3.0, d_h_a_angle_cutoff=120.0)
hb.run()

Print the results

print("Hydrogen Bonds:")
for ts, bonds in hb.timeseries.items():
print(f"Time step {ts}:")
for bond in bonds:
donor, acceptor, distance, angle = bond
print(f" Donor: {donor.resname} {donor.resid} {donor.name}")
print(f" Acceptor: {acceptor.resname} {acceptor.resid} {acceptor.name}")
print(f" Distance: {distance:.2f} Å")
print(f" Angle: {angle:.2f} degrees")
print()

[orbeckst]

I strongly suggest you have a look at the User Guide: Hydrogenbond analysis and study the Hydrogen bond analysis docs — this is a powerful and flexible but complicated analysis tool with many settings.

• Attempt 1: Your GRO file does not contain charge information, which is needed to identify donors/acceptors. Use a TPR file (when working with GROMACS) or another topology file like PSF — they should have bond information. Otherwise you have to manually define donors/acceptors.
• Attempt 2: for ts, bonds in hb.timeseries.items(): — where did you find this code? HydrogenBondAnalysis in recent versions of MDAnalysis (at least since 2.0.0) does not produce an attribute HydrogenBondAnalysis.timeseries. Instead, look in HydrogenBondAnalysis.results.hbonds but note the format of this array, it's not a dict!