Updated script reproducehbondissue.py to work with MDAnalysis 0.16.1-dev ; part of https://github.com/MDAnalysis/mdanalysis/issues/1268 .

reproducehbondissue-0.16.1.py

#! /usr/bin/env python2.7

# 0.16.1-dev

import MDAnalysis as mda
import MDAnalysis.analysis.hbonds

def select_monomers_str(u, nmer=4):
    protein = u.select_atoms("protein")
    return ["protein and bynum {0}:{1}".format(i1, i2)
            for i1 in range(1, protein.n_atoms, protein.n_atoms/nmer)
            for i2 in [i1+protein.n_atoms/nmer - 1]]


if __name__ == "__main__":
    # input
    grofile = "t39000.gro"

    # Create the md universe
    u = mda.Universe(grofile)

    # Analyze monomers separately
    # Need to use selection string for each monomer:
    monomer_selections = select_monomers_str(u)

    hbonddist = 3.0 # distance in Angstrom between donor H and acceptor atom.
    hbondangle = 180-35 # deg (different angle def in the mda hbond tool than for gmx)

    # just look at one monomer for right now;
    # To loop: for monomer_selection in monomer_selections:
    #imonomer = 0

    for monomer_selection in monomer_selections:
        sel1 = "{0} and resid 197 and name ND2".format(monomer_selection)
        hbondana = MDAnalysis.analysis.\
                   hbonds.HydrogenBondAnalysis(u, \
                                               selection1=sel1,
                                               selection2='resname SOL and name OW',
                                               selection1_type='donor',
                                               distance=hbonddist, angle=hbondangle,
                                               filter_first=True, debug=True)
        print 'running hbond ana for monomer {}'.format(monomer_selection)
        hbondana.run()