Part of issue report https://github.com/MDAnalysis/mdanalysis/issues/1268 by @vivecalindahl

reproducehbondissue.py

#! /usr/bin/env python2.7

import MDAnalysis as mda
import MDAnalysis.analysis.hbonds 

def select_monomers(u, nmer=4):
    protein = u.select_atoms("protein")

    # note: bynum is 1-based so range starts at 1
    monomers = [u.select_atoms("protein and bynum " + str(i1) + ":" + str(i2)) for i1 in range(1, protein.n_atoms, protein.n_atoms/nmer) for i2 in [i1+protein.n_atoms/nmer - 1]]
    
    # List with the monomer atom groups
    return monomers
    
def segment_monomers(u):
    monomers = select_monomers(u)
    segids = ["monomer" + str(i+1) for i in range(len(monomers))]

    for monomer, segid in zip(monomers, segids):
        monomer.segids = segid        

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

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

    # Analyze monomers separately
    segids = segment_monomers(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)
    oxygens_t_seg=[]

    #    for segid in segids:
    segid=segids[0]

    hbondana = MDAnalysis.analysis.hbonds.HydrogenBondAnalysis(u,
                                                               selection1= ' and '.join(['segid ' + segid, 'resid 197', 'name ND2']),
                                                               selection2='resname SOL and name OW',
                                                               selection1_type='donor',
                                                               distance=hbonddist, angle=hbondangle)
    print 'running hbond ana for segid ' + segid
    hbondana.run()