CHARMM c28a3 hbonds.doc

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                    Generation of Hydrogen Bonds

        The generation of hydrogen bonds is one of the major steps in
analyzing the energy of a system.  This energy term is not usually used
in minimization or dynamics because modern parameter sets compute
hydrogen bond contributions as a balance between electrostatic attraction
and van der Waal repulsion terms.  This facility remains useful for the
purpose of enery and structural analysis.  The process of hydrogen bond
generation involves looking at all possible pairs of hydrogen bond
donors and acceptors and selecting those which are "good". The meaning
of "good" is determined by parameters to be described below. In
addition, the generation routine is responsible for constructing the
positions of all uncoordinated hydrogens and adding them into the
coordinate list.

        The selection of hydrogen bonds involves three checks. First,
any good hydrogen bond has a length less than some cutoff. Second, the
angle off linearity has a value less than some cutoff. This angle is 180
- D--H...A.  Finally, if a hydrogen donor has more than one acceptor
which satisfies the above constraints and BEST is specified, the routine
will select the one with the lowest energy (normally it will take ALL
and let the minimization or dynamics adjust there strengths).

        To obtain a more detailed description of the selection process
and the process of constructing hydrogen coordinates, the CHARMM paper
should be consulted.

        Because there are cutoff's involved with the selection of
hydrogen bonds, and because the hydrogen bond list must be updated
during dynamics, and because energy must be conserved, switching
functions are needed to smooth the transition over a cutoff. Therefore,
the specification of hydrogen bond generation also allows the
specification of switching function parameters.

        One should note that particular choices for the selection
process will never conserve energy in a dynamics run. First, one must fix
the hydrogen bond list if one uses the extended atom representation.
This is necessary as one cannot apply a switching function to the
hydrogen bond angle as it is not calculated if the hydrogens are not
present. Second, the selection of the best hydrogen bond for a given
donor can't be used, because there is no switching function to smooth
the transition between two possible and mutually exclusive hydrogen

        The generation is performed by CHARMM at several different
points. One can request the hydrogen bonds be generated explicitly using
a hydrogen bond command. This is useful prior to analyzing the system.
The hydrogen bonds can be generated during any energy manipulation, see
*note Energy:(energy.doc).

* Menu:

* Syntax::              Syntax of the Hydrogen bond specification
* Function::            Purpose of each of the keywords

File: Hbonds ]-[ Node: Syntax
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                Syntax of the Hydrogen Bond Command


{ HBONds       }        { [IHBFrq integer]  hbond-spec  }
{ UPDAte ...   }        { [IHBFrq  0     ]              }
{ MINImize ... }        {                               }
{ DYNAmics ... }        {                               }
{ ENERgy ...   }        {                               }

hbond-spec ::= [BEST] [DUMMy] [CUTHB real] [CUTHBA real] [ACCE] [INIT]
               [ALL ]                                    [NOAC]

        [HBEXclude] [CTONHB real] [CTOFHB real] [CTONHA real] [CTOFHA real]
        [HBNOexcl ]

NOTE:: The IHBFrq value is remembered. If its value is zero,
interpretation of [hbond-spec] will be supressed as well as any
modifications to the hbond list.


HBTRim  real


[ DONOr    ]  [ REMOve ] atom-selection [NOANtecedents] [SHOW]
[ ACCeptors]  [ ADD    ]
              [ SET    ]

File: Hbonds ]-[ Node: Function
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            Purpose of the various hydrogen bond variables.

Variable  Default      Function

ACCE/NOAC ACCE         ACCE specifies that acceptor anticedents will be
                       used in an (H-A-AA) angle factor where present in the
                       structure file (from the RTF).

HBEX/HBNOexclude       HBEXclude causes all hydrogen bonds between excluded
                       atoms to be removed in the hbond edit facility.
                       This also includes 1-4 interaction if appropriate
                       as determined by the NBXMode nonbond value.
                       This option is needed for systems where no angle
                       cutoff is applied (as in the AMBER potential).

BEST/ALL    ALL        BEST turns on selection of best hydrogen bond for
                       a given donor. ALL takes all hydrogen bonds for
                       given donor which satisfy the other conditions.

DUMMy                  Sets CUTHB and CUTHBA to zero. This will result in
                       no hydrogen bonds which is desirable when one is
                       not interested in the hydrogen bond energy. The
                       selection will be done very quickly in this case.

CUTHB       4.5        Maximum distance allowed for a hydrogen bond. This
                       distance is measured between the heavy atoms
                       NOTE: a CUTHB value less than 1.0 will disable
                       the HBOND generation code (for efficiency).

CTOFHB    CUTHB-0.5    Distance where distance switching function is off
                       Once specified, it will only change if respecified.

CTONHB    CTOFHB-0.5   Distance where distance switching function is on.
                       Once specified, it will only change if respecified.

CUTHBA     90.0        Maximum out of line angle allowed for a hydrogen
                       bond. The angle is 180 - D--H...A angle
CTOFHA    CUTHBA-20.0  Angle where angle switching function is off
                       Once specified, it will only change if respecified.

CTONHA    CTOFHA-20.0  Angle where angle switching function is on.
                       Once specified, it will only change if respecified.

INIT      do not       INIT specifies that all values and conditions return
                       to the original defaults.

File: Hbonds ]-[ Node: HBTRim
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The HBTRim command deletes all hydrogen bonds that have an energy
of interaction that is higher than the specified cutoff.  This
command is used to reduce a list of all hydrogen bonds to that of
important hydrogen bonds.

The syntax is;

HBTRim  real

where the real value is the energy cutoff and should usually be

File: Hbonds ]-[ Node: DONOr
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[ DONOr    ]  [ REMOve ] atom-selection [NOANtecedents] [SHOW]
[ ACCeptors]  [ ADD    ]
              [ SET    ]

These commands modify the list of donors or acceptors contained
in the structure file (PSF).  By invoking this command before
the generation of a hydrogen bond list, the content of this
list can be manipulated.  The REMOve suboption will delete
any current donors/acceptors contained in the selected atoms.
The ADD suboption will create additional donors/acceptors based
on the selected atoms.  The SET suboption will revove all current
donors/acceptors and replace the list with the selected set of
      By default, any single atom bonded to a selected atom
will be included as the donor/acceptor antecedent.  To prevent
this, the NOAT keyword can be used to generate simple (radial only)
hydrogen bonds.  The SHOW keyword causes the new list of
donors/acceptors to be displayed.

See io.doc for commands that input/output HBONd information.

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