Distances hbond

distances hbond

Parameters

donors=string

(default: *)

acceptors=string

(default: *)

distance=real

(default: 3.5)

angledonor=real

(default: 90.0)

angleacceptor=real

(default: 75.0)

structures=integer

(default: none)

weight=real

(default: 1.0)

ambiguous

append

Description

This command analyzes the selected structures with respect to potential hydrogen bonds and generates upper and lower distance bounds to restrain potential hydrogen bonds.

Potential hydrogen bonds are searched between hydrogen atoms that match the donors atom selection and other atoms that match the acceptors atom selection. Only atoms that are declared as potential hydrogen donors or acceptors in the ATOMTYPES entry of the residue library are taken into consideration.

A potential hydrogen bond must fulfill the three following criteria in at least as many selected structures as defined by the structures parameter:

• The distance between the donor hydrogen and the acceptor must be

  shorter than the cutoff given by the distance parameter (in Angstrom).

• The angle at the donor hydrogen must be larger than the cutoff given

  by the angledonor parameter (in degrees).

• The angle(s) at the acceptor must be larger than the cutoff given

  by the angleacceptor parameter (in degrees).

Unambiguous hydrogen bond restraints are generated, if a donor hydrogen is involved in a single potential hydrogen bond. If several potential hydrogen bonds can be found for a donor hydrogen, then ambiguous hydrogen bond restraints are generated only if the ambiguous optionm is set.

The restraints consist of (unambiguous or ambiguous) upper distance limits of 2.0 Angstrom between the donor hydrogen and the acceptor atom and of 3.0 Angstrom between the acceptor atom and the atom that is covalently bound to the donor hydrogen. Unambiguous lower distance limits of 1.8 and 2.7 Angstrom, respectively, are generated for the same distances. The relative weight of these distance restraints can be set with the weightparameter. By default, unless the append option is set, these distance restraints replace all existing distance restraints.