hbond_analysis is a member of SPANA and the parallelized version of ‘
hb_analysis‘. This tool is parallelized with hybrid MPI/OpenMP. Like ‘
hb_analysis‘, we need the three geometrical parameters for the detection of H-bond:
HDA_angle (α), and
DHA_angle (β). In the default, d = 3.4 Å, α = 30.0 deg. and β = 120.0 deg, and if you use your own definition, you can specify these value in [HBOND_OPTION].
Hbond_analysis‘ tool is useful to examine H-bond patterns for a huge protein molecule or for crowding system. You can limit the range used for the analysis (for example, focus on H-bonds around ligand-binding site or in hydrophilic channel) by adequately using ‘
determine_box = MANUAL‘ option.
Functions of this tool is same as ‘
hb_analysis‘ except this analysis is done with space_decomposition. Thus, when you need a H-bond list written in ‘
hb_listfile‘, the hb_listfile is output per domain. When you specify ‘
hb_listfile‘ name, you need ‘()’ to return MPI process numbers. The parameter ‘
cutoff‘ is important to determine the range to search H-bond partners of ‘analysis_atom’. The ‘
cutoff‘ value should be larger than the ‘
hb_analysis‘, to wrap molecules into the PBC box, we need the use of the options ‘
recenter‘ and ‘
wrap‘ to correctly detect H-bonds formed between ‘
analysis_atom‘ and ‘
[INPUT] psffile = BPTI_ionize.psf reffile = BPTI_ionize.pdb [OUTPUT] txtfile = BPTI-wat_Hbond.txt hblist_file = BPTI_wat_hbond_mpi().list [TRAJECTORY] trjfile1 = run.dcd md_step1 = 10 mdout_period1 = 1 ana_period1 = 1 trj_format = DCD trj_type = COOR+BOX [ENSEMBLE] ensemble = NPT [BOUNDARY] type = PBC domain_x = 2 domain_y = 2 domain_z = 1 num_cells_x = 10 num_cells_y = 10 num_cells_z = 10 box_size_x = 50.0 box_size_y = 50.0 box_size_z = 50.0 [SELECTION] group1 = sid:BPTI & resno:1-58 group2 = resname:TIP3 group3 = sid:BPTI & (resno:3 | resno:7-8 | resno:39-40 | resno:43) [SPANA_OPTION] wrap = yes # wrap molecules if wrap = yes buffer = 5.0 # this distance should be larger than hb_distance. box_size = TRAJECTORY # (TRAJECTORY / MANUAL / MAX) [HBOND_OPTION] recenter = 3 output_type = count_atom # (count_atom / count_snap) analysis_atom = 1 target_atom = 2 solvent_list = TIP3 # hb_distance = 3.4 # upper limit of distance between Donor and Acceptor atoms, default value is 3.4 A # dha_angle = 30.0 # upper limit of H-bond D-H..A angle, default value is 30.0 deg. # hda_angle = 120.0 # lower limit of H-bond H-D..A angle, default value is 120.0 deg.