hbonds (c45b1)
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
bonds.
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
» energy
* Syntax | Syntax of the Hydrogen bond specification
* Function | Purpose of each of the keywords
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
bonds.
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
» energy
* Syntax | Syntax of the Hydrogen bond specification
* Function | Purpose of each of the keywords
Top
Syntax of the Hydrogen Bond Command
[SYNTAX HBONd]
{ 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.
[SYNTAX HBTRim]
HBTRim real
[SYNTAX DONOr]
[SYNTAX ACCEptor]
[ DONOr ] [ REMOve ] atom-selection [NOANtecedents] [SHOW]
[ ACCeptors] [ ADD ]
[ SET ]
Syntax of the Hydrogen Bond Command
[SYNTAX HBONd]
{ 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.
[SYNTAX HBTRim]
HBTRim real
[SYNTAX DONOr]
[SYNTAX ACCEptor]
[ DONOr ] [ REMOve ] atom-selection [NOANtecedents] [SHOW]
[ ACCeptors] [ ADD ]
[ SET ]
Top
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.
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.
Top
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
negative.
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
negative.
Top
[ 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 remove all current
donors/acceptors and replace the list with the selected set of
atoms.
By default, any single atom bonded to a selected atom
will be included as the donor/acceptor antecedent. To prevent
this, the NOAN keyword can be used to generate simple (radial only)
hydrogen bonds. The SHOW keyword causes the new list of
donors/acceptors to be displayed.
NB! All modifications listed above are strictly based on the atom-selection,
without taking into account any DONOr/ACCeptor specifications in either the PSF
or the RTF. If your selection includes aliphatic carbons they may end up as
donors/acceptors...
To add water hydrogens as hydrogen bond donors a command like this would be
used:
DONOR ADD SELECT RESN TIP3 .AND. HYDROGEN END
To remove all backbone carbonyls as acceptors:
ACCEPTOR REMOVE SELECT ATOM PROTA * O END
Substitution variables NDON/NACC are set to the resulting number of
donors/acceptors.
» io for commands that input/output HBONd information.
[ 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 remove all current
donors/acceptors and replace the list with the selected set of
atoms.
By default, any single atom bonded to a selected atom
will be included as the donor/acceptor antecedent. To prevent
this, the NOAN keyword can be used to generate simple (radial only)
hydrogen bonds. The SHOW keyword causes the new list of
donors/acceptors to be displayed.
NB! All modifications listed above are strictly based on the atom-selection,
without taking into account any DONOr/ACCeptor specifications in either the PSF
or the RTF. If your selection includes aliphatic carbons they may end up as
donors/acceptors...
To add water hydrogens as hydrogen bond donors a command like this would be
used:
DONOR ADD SELECT RESN TIP3 .AND. HYDROGEN END
To remove all backbone carbonyls as acceptors:
ACCEPTOR REMOVE SELECT ATOM PROTA * O END
Substitution variables NDON/NACC are set to the resulting number of
donors/acceptors.
» io for commands that input/output HBONd information.