CONFLEX Manual

Host-Ligand Coordination Search Keywords

Keyword	Options	Description
HLSEARCH		Host-Ligand coordination search will be performed.
HLSEARCH_HOST_POLYHEDRON=	TETRA CUBE OCTA ICOSA	Selection of the type of regular polyhedron for placing a ligand molecule. TETRA: Tetrahedral CUBE: Cubic OCTA: Octahedral ICOSA: Icosahedral Default is “ICOSA”.
HLSEARCH_HOST_NDIV=	n	The number of subdivisions of the edges. Default is 1.
HLSEARCH_LIGAND_MOL=	l	Specify l-th molecule as ligand. Default is 2.
HLSEARCH_LIGAND_ROT=	(n1,n2,n3)	Set the initial orientation of the ligand molecule rotating around x, y and z axes by 360/n1, 360/n2 and 360/n3 degrees, respectively. Default is (6,6,6).
HLSEARCH_BUFFER=	ff.ff	Distance between spheres surrounding both host molecule(s) and ligand molecule. Default value is 1.0.Å
HLSEARCH_NOT_COMPARE		All geometrical data of complex are stored without comparing the steric energies.

Molecular Object Group Option

Keyword	Options	Description
MOL_GROUP=	(i,n)	For systems composed of multiple molecules, define a molecule object group that contains one or a few molecules. For example, if you write “MOL_GROUP=(3,1)” in the ini file, all the atoms that make up the molecule to which the third atom (i=3) belongs will automatically be classified as molecule object 1 (n=1). By repeatedly using this keyword, multiple molecules can be combined into a single molecular object.
GOPT=	CONGRD NEWTON	Select a geometry optimization method for the molecular object group specified by “MOL_GROUP=”. “GOPT” without specification corresponds to “GOPT=(CONGRD,NEWTON)”.
GOPT_HYDROGENS		All hydrogens are classified and subject to optimization before optimizing the target molecular object group.
GOPT_SCF_CYCLE=	n	Maximum number of SCF cycles of molecular group optimization. Default is equal to 1.
GOPT_ECNVRG=	f.f	Energy threshold (kcal/mol) for SCF cycles of molecular group optimization. Default value is equal to 1.0D-4

Vibrational Analysis Keywords

Keyword	Options	Description
THERMO= Example: THERMO=XYZ	XYZ INTER HEVYLP	Vibrational analysis, that is equivalent to the normal mode analysis using the mass weighted second derivative matrix, will be performed if the structure enough to be optimized is given. Thermodynamics functions, the vibrational frequencies and the corresponding mass weighted vibrational modes are also printed. “XYZ” and “INTER” control the printing form in Cartesian and internal coordinate system, respectively. The default is “XYZ”. If “HEVYLP” is specified, lone pairs are packed into the elements of the second derivative matrix at the attached heavy atom. Default: XYZ
NOTHERMO		Does not perform any thermodynamic calculation and also print out any vibrational mode or eigenvectors.
EIGVEC= Example: EIGVEC=XYZ	XYZ INTER HEVYLP	Normal mode analysis without the mass weighted second derivative matrix will be performed, and then eigen values and eigen modes are written to the output file. “XYZ” and “INTER” control whether the information is written to the output file as Cartesian or Internal coordinate formats, respectively. If “HEVYLP” is specified, lone pairs are packed into the elements of the second derivative matrix at the attached heavy atom. Default is “XYZ”.
TEMP= Example: TEMP=30.0	ff.ff	Temperature is specified to ff.ff degrees centigrade (°C). Default is 25.0.
ALLMODE		Print out all vibrational modes computed.
LOWMODE=	ff.ff	Print out vibrational modes or eigenvectors that the frequencies or eigenvalues are less than ff.ff.
NOMODE		Thermodynamic calculation will be performed, but never been printed any vibrational mode or eigenvectors.
PROJECT_OUT= Example: PROJECT_OUT=6	n	Remove vibration modes where the frequency is close to 0.0.

PDB File loading options

Keyword	Options	Description
PDB_MUTATE=	(resname,chain,num)	One amino residue having chain of chain ID and num of residue number described in PDB file can be replaced to a standard amino residue specified by resname of the amino residue. Elongation of the sidechain will be automatically folded by minimizing the following evaluation function: where r_i is a non-bonded distance between an elongated atom i and the other atom, R and k are the considerable distance threshold and the force constant, respectively. Name of amino residues for resname can be described by using any type of three nomenclatures: one character (A, N, C, E, H, etc.), three characters (ALA, ASN, CYS, GLU, HIS, etc.), and full-name of amino acid (alanine, asparagine, cysteine, gulutamic_acid, histidine, etc.).
PDB_NOMUTATE		Missing atoms of amino residue are not added. Therefore, “PDB_MUTATE=” option must be required for the correct application of computational chemistry to peptides and proteins.
PDB_THRESH=	R	Distance threshold in Å.
PDB_KCONST=	k	Force constant in kcal/mol/Å²
PDB_HETATM		All atoms in “HETATM” records are considered for calculation. (default)
PDB_NOHETATM		All atoms in “HETATM”records are ignored.
PDB_WATER		“HOH” atoms in “HETATM” records are used for calculation. (default)
PDB_NOWATER		“HOH” atoms in “HETATM” records are ignored.
PDB_MODEL_NO=	n	Selection of the model serial number that specifies an ensemble to. Default is the first model that is corresponding to “PDB_MODEL_NO=1”. If no entry of “MODEL” record in the PDB file, all atoms are used for calculation.
PDB_SSBOND		Connect the S-S bonds that are specified in “SSBOND” record.
PDB_NOSSBOND		All “SSBOND” records are ignored.
PDB_SSB_DIST=	ff.f	Distance threshold of S-S bond connection
PDB_CONECT=	(I,J,K)	Bonding between I and J atoms with K-bond type: K=1: Single bond K=2: Double bond K=3: Triple bond K=4: Ionic bond (I+,J-)
PDB_DISCONECT=	(I,J)	A bond between I and J atoms is forcibly disconnected.
PDB_CHARGE=	(I,K)	Put a formal charge K on I atom. For example, to specify a formal charge of +2 for a calcium ion with atom No.1354, the keyword description would be “PDB_CHARGE=(1354,+2)”.