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MM model description and initialization |
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typedef vector< MatPoint * > | POINTS_TYPE |
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| HaMolMechMod (HaMolSet *new_pmset=NULL) |
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int | SetStdParams () |
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int | Initialize () |
| | Init module - build MM model and force field.
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int | SetStdValParams () |
| | Set Standard parameters for valence bonds, angles and dihedrals.
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int | SetStdVdWParams () |
| | Set Standard Van-der-Waals parameters.
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bool | BuildExcludedAtomList () |
| | Build the excluded atom list.
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bool | BuildNonBondContactList () |
| | Build the non-bonded contact list.
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bool | BuildGrpGrpNonBondList (AtomList *group1, AtomList *group2) |
| | Build a non-bonded contact list for atoms theat belong to two groups.
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virtual int | OnDelAtoms (AtomCollection &del_atoms) |
| | Modify module content to react to deleted atoms (from HaCompMod).
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bool | DeletePoints (set< MatPoint *, less< MatPoint * > > *pt_set) |
| | Delete list of Points from the module.
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bool | Print_info (ostream &sout, const int level) |
| | Print various info.
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MMBond * | GetMMBond (MatPoint *pt1, MatPoint *pt2) |
| | get bond between points
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MMValAngle * | GetValAngle (MatPoint *pt1, MatPoint *pt2, MatPoint *pt3) |
| | get valence angle between points
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MMDihedral * | GetDihedral (MatPoint *pt1, MatPoint *pt2, MatPoint *pt3, MatPoint *pt4) |
| | get dihedral angle for points
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MMDihedral * | GetImprDihedral (MatPoint *pt1, MatPoint *pt2, MatPoint *pt3, MatPoint *pt4) |
| | get dihedral angle for points
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vector< SetMatPt > | excluded_atom_list |
| | Excluded atom list: atoms for which non-bonded calculations are not computed.
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vector< SetMatPt > | nonbond_contact_list |
| | Non-bonded contacts lists: atoms for which non-bonded interactions are computed.
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vector< MatPoint * > | Points |
| | MatPoints - Atoms and other force and mass centers.
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set< MMBond, less< MMBond > > | MBonds |
| | Bonds.
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set< MMValAngle, less< MMValAngle > > | ValAngles |
| | Valence angles.
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vector< MMDihedral > | Dihedrals |
| | Dihedrals.
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vector< MMDihedral > | ImprDihedrals |
| | Improper dihedral angles.
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vector< MMBond > | BondConstrains |
| | Harmonic constraints.
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multimap< unsigned long, unsigned
long, less< unsigned long > > | res_impr_dih_map |
| | map of Improper angles arranged by the residue of the 3rd atom
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list< MMNonBndParam > | HBondParams |
| | Hydrogen Bonds parameters.
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Setting Force Field Parameters: |
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MMDihedral * | AddImprDihedral (MatPoint *pt1, MatPoint *pt2, MatPoint *pt3, MatPoint *pt4) |
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int | SetMMBond (MatPoint *pt1, MatPoint *pt2, double r0, double fc, int set_type=NOT_SET) |
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int | SetValAngle (MatPoint *pt1, MatPoint *pt2, MatPoint *pt3, double a0, double fc, int set_type=NOT_SET) |
| | set valence angles
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| int | GetResImprAngles (HaResidue *pres, list< MMDihedral * > &res_idih_list) |
| int | Set14interDihFlags () |
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HaVec_double | FindPointParamFromSymbol (const char *ats1) |
| | Find Force Field atom parameters for FFSymbol.
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HaVec_double | FindBondParamFromSymbol (const char *ats1, const char *ats2) |
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HaVec_double | FindValAngleParamFromSymbol (const char *ats1, const char *ats2, const char *ats3) |
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HaVec_double | FindDihedralParamFromSymbol (const char *ats1, const char *ats2, const char *ats3, const char *ats4, bool improper_flag=false) |
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StrVecMap | symb_ppar_map |
| | Map strings to VdW atom parameters.
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StrVecMap | bond_param_map |
| | Map strings to Valence Bonds parameters.
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StrVecMap | vang_param_map |
| | Map strings to Valence Angles parameters.
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StrVecMap | dih_param_map |
| | Map strings to Dihedral Angles parameters.
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StrVecMap | impdih_param_map |
| | Map strings to Improper Dihedral Angles Parameters.
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int | init_ff_maps = FALSE |
| | Flag to indicate that Force-Field symbol to parameters maps were initiated.
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Molecular Mechanics run parameters: |
| int | InitParamSet () |
| | Initialize Force-Field parameters.
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int | cur_nstep |
| | Current num step of Minimization of MD trajectory.
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double | time |
| | Current trajectory time.
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double | temp |
| | Current simulation temperature.
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double | press |
| | Current pressure in MD.
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double | cur_energy |
| | Current computed MM energy (kcal/mol).
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double | kin_ene |
| | Current kinetic energy.
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double | pot_ene |
| | Current Potential energy.
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double | bond_ene |
| | Current Valence Bond energy.
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double | vang_ene |
| | Valence Angle Energy.
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double | dihed_ene |
| | Current Dihedral Angle energy.
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double | vdw_ene |
| | Current VdW energy.
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double | vdw_ene_14 |
| | Current VdW 1-4 energy.
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double | vdw_ene_nb |
| | Current VdW not 1-4 energy.
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double | electr_ene |
| | Current Electrostatic energy.
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double | electr_ene_14 |
| | Current Electrostatic 1-4 energy.
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double | electr_ene_nb |
| | Current Electrostatic non 1-4 energy.
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double | polar_ene |
| | Polarization energy.
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double | hbond_ene |
| | Energy of H-bonds.
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double | constraint_ene |
| | Energy of constraints.
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double | density |
| | Average density in g/mL.
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double | rms_ene |
| | RMS of energy during optimization.
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double | grad_ene_max |
| | Maximum gradient of energy during optimization.
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int | module_to_init_flag |
| | Flag to initiate module sturctures at the next calls to module functions.
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int | build_nb_contact_list_flag |
| | Flag to build non-bond contact list during initialization of the module.
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int | param_to_init_flag |
| | Flag to indicate that Force-Field parameters have been set.
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int | init_charges_flag |
| | if true, attempt to set charges on the atoms during initialization if they are zero
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AMBER input and output files: |
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int | SaveAmberRunFile () |
| | Save script to run AMBER on UNIX.
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int | SaveAmberInpFile () |
| | Save AMBER input parameters file.
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int | SaveAmberTopFile () |
| | Save AMBER topology file (*.top).
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int | SaveAmberCrdFile () |
| | Save file with initial coordinates.
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int | SaveAmberAllInpFiles () |
| | Save all AMBER input files.
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HaString | amber_run_file |
| | Name of AMBER UNIX run file.
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HaString | amber_inp_file |
| | Name of AMBER input file.
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HaString | amber_top_file |
| | Name of AMBER topology file.
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HaString | amber_crd_file |
| | Name of AMBER initial coordinates file.
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HaString | amber_out_file |
| | Name of the Amber out file.
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HaString | amber_rst_file |
| | Name of AMBER restart file.
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HaString | amber_trj_coord_file |
| | Name of the AMBER MD coordinates trajectory file.
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HaString | amber_trj_vel_file |
| | Name of the AMBER MD velocity trajectory file.
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HaString | amber_trj_ene_file |
| | Name of the AMBER MD energy trajectory file.
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HaString | amber_constr_crd_file |
| | Name of the AMBER coordinates constraints file.
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FILE * | trj_coord_fp |
| | File pointer for AMBER MD coordinates trajectory file.
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FILE * | trj_vel_fp |
| | File pointer for AMBER MD velocities trajectory file.
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FILE * | trj_ene_fp |
| | File pointer for AMBER MD velocities trajectory file.
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MM run control |
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int | RunSanderInt () |
| | Run Internally linked SANDER.
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int | LoadAmberRestartFile () |
| | Load coordinated from the AMBER restart file.
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int | LoadAmberMDInfoFile () |
| | Load info from AMBER mdinfo file.
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int | RunAmber () |
| | Run AMBER simulations (Sander).
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int | RunAmberThread () |
| | Functions called by RunAmber that actually do the work as a separate thread.
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int | OpenSanderFilesToRead () |
| | Open Sander trajectory files to prepare reading trajectory.
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int | ReadTrajPoint () |
| | Read next AMBER trajectory point.
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int | StopCalc () |
| | Stop Molecular Mechanics Calculations.
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| int | CalculateEnergy () |
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bool | CalcNonBondPt (const MatPoint *pt1, const MatPoint *pt2, double &vdw_at_ene, double &el_at_ene) |
| | calculate nonbonding energy between two MatPoints
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int | run_internal_flag |
| | if TRUE run MM calculation internally
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HaString | sander_exe_fname |
| | AMBER(sander) executable file name.
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HaString | traj_script |
| | Python script to execute at points of trajectory.
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long | amber_proc_id |
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CWinThread * | run_amber_thread |
| | Windows thread controlling AMBER simulations.
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int | delay_time |
| | delay time between steps in ms
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int | stop_calc_flag |
| | it not zero stop MM calculations
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int | skip_pt_init |
| | The number of trajectory points to skip in the beginning of the trajectory.
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int | skip_pt_between |
| | The number of trajectory points to skip between points displayed and processed.
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int | play_back_flag |
| | if TRUE playback saved trajectory
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Restraints and Belly dynamics control: |
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int | SetMoveOnly (const HaString &new_mov_atom_list_name) |
| | Froze positions of all atoms except of the specified atom_list (belly dynamics).
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int | SetMoveAll () |
| | Unfroze all atoms.
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AtomList * | GetMovingAtoms () |
| | Get Atom List of atoms allowed to move (=NULL if all atoms allowed to move).
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int | SetRestrainedAtoms (const char *restr_atom_list_name) |
| | set name of atom list of harmonically restrained atoms
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AtomList * | GetRestrAtoms () |
| | Get Atom List of atoms with harmonically restrained positions.
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bool | SetHBondConstraints (double force_const ) |
| | put harmonic constraints on the H-Bonds
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int | AddHarmConstraint (HaAtom *atom1, HaAtom *atom2, double eq_dist, double force_const ) |
| | Add Harmonic Constraint.
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bool | ClearConstraints () |
| | Delete All Harmonic constraints.
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double | atom_restr_const |
| | force constant for atom position restraints (kcal/mol/Ang^2)
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HaString | moving_atoms |
| | name of the atom list of atoms allowed to move in the dynamics =ALL_ATOMS for normal runs
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HaString | restrained_atoms |
| | name of the atom list of restrained atoms in Constrained Dynamics
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General MM Execution params: |
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int | time_limit |
| | time limit of the job in sec, TIMLIM in AMBER
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int | run_type |
| | correspond to imin parameter in AMBER
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int | nmr_restrain |
| | NMR restrain param, NMROPT in AMBER.
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int | amber_version |
| | version of the AMBER program
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input coord and vel params: |
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int | init_read_coord |
| | type of initial coord - corresponds to NTX in Amber
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int | restart_flag |
| | restart job - IREST in AMBER
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int | restraint_format |
| | format of restraint file - NTRX in AMBER
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output params: |
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int | write_coord_format |
| | format of final coord and vel output, NTXO in AMBER
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int | print_freq |
| | Print frequency to the ouput file, NTPR parameter of AMBER.
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int | nbstp_wrt_rstrt |
| | frequency to write restart file NTWR parameter
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int | nbstp_wrt_coord |
| | frequency to write coord file NTWX parameter
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int | nbstp_wrt_vel |
| | frequency to write velocities file NTWV parameter
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int | nbstp_wrt_ener |
| | frequency to write energy file NTWE parameter
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int | traj_wrt_format |
| | format of the written trajectory, corresponds to AMBER IOUTFM
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| int | limit_wrt_atoms |
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int | wrap_coord |
| | corresponds to amber IWRAP
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Potential function: |
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int | omit_interactions |
| | NTF in AMBER.
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int | period_bcond |
| | periodical boundary conditions, NTB parameter in AMBER
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int | electr_model |
| | model to treat electrostatic interactions
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double | scale_14_electr |
| | Scale coef (descrease) 1-4 coulomb inter.(SCEE parameter in AMBER).
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double | scale_14_vdw |
| | Scale coef (descrease) 1-4 vdw inter ( SCNB parameter in AMBER).
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double | nonb_cutoff_dist |
| | cutoff distance for non-bond interactions, CUT in AMBER
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double | diel_const |
| | Dielectric constant, DIELC in AMBER.
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int | nonb_list_flag |
| | Flag to generate non-bonded atom list, NTNB in AMBER.
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int | nonb_list_update_freq |
| | Frequency to update non-bonded atoms list, NSNB in AMBER.
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int | water_pairlist_method |
| | method to generate water pairlist, NTID in AMBER
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int | neutral_end_hydr_flag |
| | neutralize end hydrogen (needed for DNA) ICHDNA in AMBER
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int | calc_vdw_flag |
| | Flag to compute Van-der-Waals interactions.
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int | calc_electr_flag |
| | Flag to compute Electrostatic interactions.
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int | soft_repulsion |
| | Soft repulsions option, ISFTRP in AMBER.
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| double | soft_repulsion_const |
| int | polar_method |
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int | num_3body_inter |
| | The number of 3body interactions to be defined, N3B in AMBER.
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int | num_ions |
| | The number of ions, NION in AMBER.
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[NOHEADER] |
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HaVec_int | atom2_3body |
| | AT1(I) in AMBER.
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HaVec_int | atom3_3body |
| | AT2(I) in AMBER.
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HaVec_double | pexp_3body |
| | ACON(I) in AMBER.
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HaVec_double | beta_3body |
| | BETA3(I) in AMBER.
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HaVec_double | gamma_3body |
| | GAMMA3(I) in AMBER.
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Energy minimization parameters: |
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int | min_type |
| | correspond to NTMIN parameter in AMBER
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int | max_comp_cycles |
| | MAXCYC in AMBER.
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int | num_step_steep_descent |
| | NCYC in AMBER.
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double | init_min_step |
| | Minimal minimization step, DX0 in AMBER.
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double | max_min_step |
| | Maximal minimization step, DXM in AMBER.
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double | min_cnvrg_criterium |
| | Convergence criteria for energy gradient, DRMS in AMBER.
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MD parameters: |
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int | num_md_run |
| | Number of MD runs, NRUN in AMBER.
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int | length_md_run |
| | The length of the MD run, NSTLIM in AMBER.
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| int | num_dfreedom_sub |
| int | remove_init_motion_flag |
| | motion, NTCM in AMBER
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| int | remove_motion_freq |
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int | start_vel_method |
| | Methods to generate start velocity, INIT in AMBER.
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double | start_time |
| | Start time of the trajectory, T in Amber.
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double | md_time_step |
| | MD time step(ps), DT in AMBER.
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Temperature regulation |
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double | ref_temp |
| | Reference temperature to keep system, TEMP0 in AMBER.
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double | init_temp |
| | Initial temperature, TEMPI in AMBER.
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int | random_seed |
| | IG in AMBER.
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double | scale_init_vel |
| | HEAT in AMBER.
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| int | temp_scale_method |
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int | last_solute_atom |
| | last solute atom. ISOLVP in AMBER
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double | temp_deviation |
| | DTEMP in AMBER.
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double | temp_relax_time_solute |
| | TAUTP in AMBER.
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double | temp_relax_time_solvent |
| | TAUTS in AMBER.
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double | vel_limit |
| | velocity limit, VLIMIT in AMBER
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PEACS temperature algorithm |
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double | peaks_rate |
| | TAUV0 in AMBER.
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double | peaks_coupling |
| | TAUV in AMBER.
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double | peaks_init_pot |
| | VZERO in AMBER.
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Pressure regulation: |
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int | pressure_reg_method |
| | Pressure regulation method , NTP in AMBER.
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double | ref_pressure |
| | Reference pressure, PRES0 in AMBER.
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double | compressibility |
| | compressibility in 1.0E-06/bar(water), COMP in AMBER
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double | pressure_relax_time |
| | Pressure relaxation time (in ps), TAUP in AMBER.
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int | pressure_scale_method |
| | Method for pressure scaling, NPSCAL in AMBER.
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SHAKE bond length constraints: |
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int | shake_constr |
| | Shake bond constrain option, NTC in AMBER.
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| double | shake_tol |
Special Water treatment: |
| int | solute_solvent_image_flag |
| | if = 0, IMGSLT = 1
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| int | remove_solute_nb_cut_flag |
| int | fast_water_method |
| | of TIP3P waters, JFASTW in AMBER
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HaString | wat_res_name |
| | WATNAM in AMBER.
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HaString | wat_ox_name |
| | OWTNM in AMBER.
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HaString | wat_h1_name |
| | HWTNM1 in AMBER.
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HaString | wat_h2_name |
| | HWTNM2 in AMBER.
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Water cap treatment: |
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int | water_cap_flag |
| | Flag to control Cap option, correspond to IVCAP in AMBER.
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int | cap_atom_num |
| | the Cap atom pointer(serial num) MATCAP in AMBER
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| double | cap_fconst |
NMR Refinement options: |
| int | noesy_vol_freq |
| int | nmr_penalty_min_method |
| int | nmr_max_num_submol |
Particle Mesh Ewald: |
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int | pmesh_ewald_flag |
| | Turns on the Particle Mesh Ewald, IEWALD in AMBER.
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double | pme_box_x |
| | Unit cell parameters for PME calculations (Ang).
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double | pme_box_y |
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double | pme_box_z |
| | BOXX, BOXY, BOXZ in AMBER.
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double | pme_box_alpha |
| | PME unit cell angles (in degrees).
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double | pme_box_beta |
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double | pme_box_gamma |
| | ALPHA, BETA, GAMMA in AMBER.
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int | pme_grid_nx |
| | size of charge grid in PME calculations
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int | pme_grid_ny |
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int | pme_grid_nz |
| | NFFTX,NFFTY,NFFTZ in AMBER.
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int | pme_spline_order |
| | the order of the B-spline interpolation in PME, SPLINE_ORDER in AMBER
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int | pme_neutralize_system |
| | Force neutralization of the unit cell, ISCHARGED in AMBER (reverse 0 - 1).
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int | pme_verbose |
| | turn on voluminous output of info about PME run, VERBOSE in AMBER
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int | exact_ewald_flag |
| | Calculate Ewald calculation is run, EXACT_EWALD in AMBER.
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double | pme_dsum_tol |
| | The width of the direct sum part of the Ewald sum, DSUM_TOL in AMBER.
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1.3.6