hamolmech.h File Reference

#include "hastl.h"
#include "hastring.h"
#include "command.h"
#include "hacompmod.h"
#include "halinalg.h"
#include "vec3d.h"
#include "haatom.h"

Go to the source code of this file.

Classes
class	MMBond
	Valence bond in the Molecular mechanics model. More...
class	MMNonBndParam
	Non-bonded (VdW) parameter in Molecular Mechanics model. More...
class	MMValAngle
	Valence Angle in Molecular Mechanics Module. More...
class	MMDihedral
	Dihedral Angle in Molecular Mechanics Module. More...
class	HaMolMechMod
	Computational module to perform Molecular Mechanics computations. More...
struct	files_type
Defines
#define	AMBER_INT   1
Typedefs
typedef set< MatPoint *, less< MatPoint * > >	SetMatPt
Enumerations
enum	SET_METHOD {   NOT_SET = 0, SET_DEFAULT = 1, SET_FF_FIELD = 2, SET_RES_TEMPL = 3,   SET_SPEC = 4 }
Functions
void	sandermn_ (doublereal *x, integer *ix, integer *ih, integer *ipairs, doublereal *r_stack, integer *i_stack)
Variables
const int	MD_RUN = 0 MIN_RUN = 1 ENER_RUN = 2
const int	NO_NMR_RESTRAIN
const int	CONJ_GRAD = 0 STEEPEST_DESCENT = 2
const int	NO_PERIODICITY = 0 CONST_VOL = 1 CONST_PRES = 2
const int	NO_BORN = 0 PAIR_GEN_BORN = 1 VACUUM = 2 DIST_DEPEND_DIEL = 3
	igb in AMBER
const int	WRT_FORM = 0 WRT_BIN = 1
	for traj_wrt_format, IOUTFM in AMBER
const int	READ_X_FORM = 1 READ_X_BIN =2 READ_XV_BIN = 4 READ_XV_FORM = 5 READ_XVBOX_BIN=6 READ_XVBOX_FORM = 7
	NTX in AMBER.
const int	NO_RESTART = 0 DO_RESTART=1
const int	RESTRAINT_BIN = 0 RESTRAINT_FORM =1
const int	WRITE_X_BIN = 0 WRITE_X_FORM = 1
const int	CALC_ALL_INTER
const int	WATER_PAIRLIST_OXYGEN = 0 WATER_PAIRLIST_ATOMS = 86
const int	DIST_DEP_DIEL = 0 CONST_DIEL = 1 GEN_BORN = 2
const int	NO_SOFT_REPULSION
const int	NO_POLAR = 0 ATOM_POLAR = 1 T3BODY_POLAR = 2
const int	MAXWELL_START_VEL = 3 READ_START_VEL = 4
const int	CONST_ENE_MD
const int	NO_CONST_P = 0 ISOTROP_CONST_P=1 ANISOTROP_CONST_P=2
const int	ATOM_PRESS_SCALE = 0 MOL_PRESS_SCALE=1
const int	NO_SHAKE = 1 H_ATOM_SHAKE=2 ALL_ATOM_SHAKE=3
const int	NORMAL_FAST_WATER
const int	NMR_ABS_VAL_ERR = 1 NMR_SQ_SUM_ERR = 2 NMR_NOESY_PENALTY = 3
	for nmr_penalty_min_method, IPNLTY in AMBER
const int	CALC_VDW_NO = 0 CALC_VDW_NORMAL = 1 CALC_VDW_NO_ATTRACT = 2
	for calc_vdw_flag
const int	SCRIPT_CONTINUE = 0
const int	SCRIPT_START = 1
const int	SCRIPT_STOP = 2
files_type	files_

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Detailed Description

Classes to perform Molecular Mechanics simualtions in HARLEM

Author:

Igor Kurnikov

Date:

1999-2002

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Variable Documentation

const int NO_NMR_RESTRAIN

Initial value: 0 READ_NMR_RESTRAIN=1 NOESY_NMR_RESTRAIN = 2

const int CALC_ALL_INTER

Initial value: 1 OMIT_BONDS_H = 2 OMIT_BONDS = 3 OMIT_BONDS_VANG_H = 4 OMITS_BONDS_VANG = 5 OMIT_BONDS_VANG_DIH_H = 6 OMIT_BONDS_VANG_DIH = 7

const int NO_SOFT_REPULSION

Initial value: 0 SOFT_REPULSION_NO_HBOND = 1 SOFT_REPULSION_ALL = 2

const int CONST_ENE_MD

Initial value: 0 CONST_TEMP_UNIFORM = 1 CONST_TEMP_SOLUTE = 2 CONST_TEMP_THRESH = 3 CONST_TEMP_QUICK_RESCALE = 4 CONST_TEMP_SOLUTE_SOLV = 5 CONST_TEMP_MAXWELL = -1

const int NORMAL_FAST_WATER

Initial value: 0 REDEF_WATER_NAMES = 1 ONLY_SHAKE_FAST_WATER = 2 ONLY_SHAKE_FAST_WATER_REDEF_NAMES = 3 NO_FAST_WATER = 4

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