HBONDS

 NAME
HBONDS – Compute solute H-bonds structural properties

 SYNOPSIS

HBONDS
    ...
    ...
END

 DESCRIPTION
The command HBONDS opens an environment which includes a series of subcommands which allow to compute hydrogen bond related properties. The hydrogen bond donor-acceptor pairs must be defined in the topological file. (see section 10.3). If these definition where not included when generating the trajectory file, and if READ_TPGPRM is specified in the &PARAMETERS environment, HBONDS produces no output. These definitions may be provided at analysis time by the READ_TPG (&PARAMETERS) directive. In the following we indicate with the letters $A$ and $D$ the donor and acceptor pair.

 angular_cutoff cutoff1 [cutoff2]
defines two angular cutoffs (in degrees) for $A...H-D$ and $A-D...H$, respectively. If only one argument is specified, the two cutoff are equal.

 histogram fbin
define the bin size (in Å) for hydrogen bonds histograms.

 print   nprint   OPEN filename
print hydrogen bond output to file filename every nprint configurations. The output format depends on READ_PDB (&SETUP) directive. If this directive is specified the output contains details concerning atomic types, hydrogen bond distances and angles.

 print_histo   nprint   OPEN filename
print hydrogen histogram to file filename every nprint configurations

 radial_cutoff cutoff
define the radial cutoff (in Å) for the hydrogen bond.

 residue
printout hydrogen bonds per residues.

 total
printout the total number of hydrogen bonds (the default)

 use_neighbor  nconf  rcut
compute neighbor list for hydrogen bonds. nconf defines how frequently the neighbor list must be computed; rcut defines the radius of the neighbor list sphere.

 EXAMPLES

   HBONDS 
     total 
     residues
     radial_cutoff 2.5
     angular_cutoff 200.0  200.0 
     print 10 OPEN test.hbnd
     histogram 0.1
     use_neighbors  5 5.0
     print_histo 2 OPEN test.hst         
   END

 WARNINGS
residue and total are ineffective when READ_PDB is also specified. Experimental - Unsupported