CHARMM Element doc/hbonds.doc 1.1#File: Hbonds, Node: Top, Up: (chmdoc/commands.doc), Next: Syntax Generation of Hydrogen Bonds The generation of hydrogen bonds is one of the major steps inanalyzing the energy of a system. This energy term is not usually usedin minimization or dynamics because modern parameter sets computehydrogen bond contributions as a balance between electrostatic attractionand van der Waal repulsion terms. This facility remains useful for thepurpose of enery and structural analysis. The process of hydrogen bondgeneration involves looking at all possible pairs of hydrogen bonddonors and acceptors and selecting those which are "good". The meaningof "good" is determined by parameters to be described below. Inaddition, the generation routine is responsible for constructing thepositions of all uncoordinated hydrogens and adding them into thecoordinate list. The selection of hydrogen bonds involves three checks. First,any good hydrogen bond has a length less than some cutoff. Second, theangle 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 acceptorwhich satisfies the above constraints and BEST is specified, the routinewill select the one with the lowest energy (normally it will take ALLand let the minimization or dynamics adjust there strengths). To obtain a more detailed description of the selection processand the process of constructing hydrogen coordinates, the CHARMM papershould be consulted. Because there are cutoff's involved with the selection ofhydrogen bonds, and because the hydrogen bond list must be updatedduring dynamics, and because energy must be conserved, switchingfunctions are needed to smooth the transition over a cutoff. Therefore,the specification of hydrogen bond generation also allows thespecification of switching function parameters. One should note that particular choices for the selectionprocess will never conserve energy in a dynamics run. First, one must fixthe hydrogen bond list if one uses the extended atom representation.This is necessary as one cannot apply a switching function to thehydrogen bond angle as it is not calculated if the hydrogens are notpresent. Second, the selection of the best hydrogen bond for a givendonor can't be used, because there is no switching function to smooththe transition between two possible and mutually exclusive hydrogenbonds. The generation is performed by CHARMM at several differentpoints. One can request the hydrogen bonds be generated explicitly usinga hydrogen bond command. This is useful prior to analyzing the system.The hydrogen bonds can be generated during any energy manipulation, see*note Energy:(chmdoc/energy.doc).* Menu:* Syntax:: Syntax of the Hydrogen bond specification* Function:: Purpose of each of the keywords#File: Hbonds, Node: Syntax, Up: Top, Next: Function, Previous: 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 anymodifications to the hbond list.[SYNTAX HBTRim]HBTRim real[SYNTAX DONOr][SYNTAX ACCEptor][ DONOr ] [ REMOve ] atom-selection [NOANtecedents] [SHOW][ ACCeptors] [ ADD ] [ SET ]#File: Hbonds, Node: Function, Up: Top, Previous: Syntax, Next: HBTRim Purpose of the various hydrogen bond variables.Variable Default FunctionACCE/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 angleCTOFHA 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, Up: Top, Previous: Function, Next: DONOrThe HBTRim command deletes all hydrogen bonds that have an energyof interaction that is higher than the specified cutoff. Thiscommand is used to reduce a list of