Opening universe described in HBondAnalysis docs causes error

[jdetle]

Expected behaviour

Running HBondAnalysis as specified in the docs should work as expected, if I am missing something simple please let me know.

Actual behaviour

Code to reproduce the behaviour

import MDAnalysis as mda
u = mda.Universe(PSF, PDB)
....

Current version of MDAnalysis:

0.14.1-dev0

[kain88-de]

Do PSF and PDB contain the same protein? It looks like we are trying to read more atoms from the PDB then we actually allocated from the PSF topology.

[richardjgowers]

Yeah the PDB file is much longer (it's solvated), I think PSF DCD is the correct combination

[jdetle]

Okay this is an error in the Docs, I'll go ahead and change PDB to DCD. This will be solved by #833.

[kain88-de]

Thanks.

[orbeckst]

I think PSF DCD is the correct combination

@jdetle also noted that the example wrongly suggests one could use the PSF/DCD combo to analyze water-protein hydrogen bonds. But the PSF/DCD combo was simulated in implicit solvent and does not have TIP3 water inside.

Instead use something like the following example where we calculate the average number of hydrogen bond for protein residues that are solvent-exposed:

import numpy as np
import MDAnalysis as mda
from MDAnalysis.tests.datafiles import GRO, XTC
from MDAnalysis.analysis.hbonds import HydrogenBondAnalysis

u = mda.Universe(GRO, XTC)

# hydrogen bonds
H = HydrogenBondAnalysis(u, 'protein', 'resname SOL', distance=3, angle=120)
H.run()
counts = H.count_by_time()
print(counts.count)
# [586 594 577 588 573 610 599 596 598 602]

# exposed residues (quick to write, slow to execute...)
Nres_exposed = np.array([u.select_atoms("protein and around 3 resname SOL").n_residues for ts in u.trajectory], dtype=np.float64)

# hbonds per residue
avg_hbonds = counts.count/Nres_exposed

# plot
import matplotlib.pyplot as plt
plt.matplotlib.style.use('ggplot')
fig = plt.figure(figsize=(5,5))
ax = fig.add_subplot(111)
ax.fill_between(counts.time, avg_hbonds, color="blue", alpha=0.3)
ax.set_xlabel(r"time $t$ (ps)")
ax.set_ylabel(r"mean number of hydrogen bonds protein-water $\langle N \rangle$")
fig.savefig("adk_avg_protein_water_hbonds.png")

[orbeckst]

@jdetle, will this be fixed with PR #833?

[jdetle]

Yep!
On Fri, May 6, 2016 at 2:07 PM Oliver Beckstein notifications@github.com
wrote:

@jdetle https://github.com/jdetle, will this be fixed with PR #833
#833?

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#838 (comment)

Have a wonderful day,
John J. Detlefs