THINK Theory Manual

Chapter 9

Appendix A Parameter File Formats

The initial letter of all variable names in the following descriptions indicates the type of variable:

C for a character variable
I for an integer variable
R for a floating point variable
X, Y, Z for coordinates (floating point variables)

Blank records and records beginning with “!” are skipped when the file is read.

A.1 Atom Types

Data:

CELEM, CTYPE, IVALEN, INUMB, ICOLOR, IATTRIB, IFORMQ, IGROUP, ICONN, RRAD, RWEIGT, RENEG, REVDW

Format:

A4, 1X, A4, I3, I4, I3, I9, 3I3, F6.2, F8.2, F5.1, F7.3

Description:

CELEM

Element symbol

CTYPE

Atom type

IVALEN

Valency

INUMB

Atomic number

ICOLOR

Colour number (1-16):
	1	blue	9	light blue
	2	green	10	light green
	3	cyan	11	light cyan
	4	red	12	light red
	5	magenta	13	light magenta
	6	brown	14	yellow
	7	white	15	peak white
	8	dark grey	16	black

IATTRIB

Attribute bit mask:
	1	aromatic
	2	delocalised
	4	H-bond donor
	8	H-bond acceptor
	16	conjugated
	32	positive charge centre
	64	negative charge centre
	128	aromatic ring centroid
	256	lipophile
	512	acidic
	1024	basic
	2048	user-defined centre type 1
	4096	lone-pair donor (Lewis base)
	8192	metal
	16384	user-defined centre type 4

IFORMQ

Formal charge

IGROUP

Group or row in periodic table (1-13), corresponding to the numbers used for the 2D search wildcard atom types (see section 8.1)

ICONN

Number of connected atoms

RRAD

F6.2

VdW radius

RWEIGT

F8.2

Atomic weight

RENEG

F5.1

Electronegativity

REVDW

F7.3

VdW e term (see section 8.5)

A.2 Bond Parameters

Data:

CTYPE1, CTYPE2, IORDER, RLEN, RCONST

Format:

A4, 1X, A4, I3, F7.3, F9.2

Description:

CTYPE1

Atom type for first atom defining bond

CTYPE2

Atom type for second atom defining bond

IORDER

Bond order:
	1	single
	2	aromatic
	8	double
	16	triple

RLEN

F7.3

Ideal bond length

RCONST

F9.2

Force constant

CTYPE1 and CTYPE2 must be atom types, not element symbols
CTYPE1 and CTYPE2 must be specified in ascending order (ie CTYPE2 ³ CTYPE1), based on the position of CTYPE1 and CTYPE2 in the atom type parameter file
The file must contain ascending values of CTYPE1
Records in the file must be sorted according to the value of CTYPE1

A.3 Angle Parameters

Data:	CTYPE, RANGLE, RCONST, RCOS
Format:	A4, 2F7.1, F9.4
Description:
	CTYPE	A4	Atom type
	RANGLE	F7.1	Ideal bond angle (in degrees)
	RCONST	F7.1	Force constant
	RCOS	F9.4	Cosine of RANGLE

CTYPE must be an atom type, not an element symbol

A.4 Ring Coordinates

Data:

ISIZE, IORDER, CELEM, X, Y, Z

Format:

2I3, 1X, A4, 3F8.3

Description:

ISIZE

Number of atoms in ring, or 0 for next ISIZE-1 records

IORDER

Bond order for bond between atoms n and n+1 in ring:
	1	single
	2	aromatic
	8	double
	16	triple

CELEM

Element for atom n

X, Y, Z

3F8.3

XYZ coordinates

The ring coordinates parameter file is divided into blocks of records; each block defining one ring and containing one record per atom in the ring. A non-zero value of ISIZE indicates the beginning of a ring definition; all remaining records in that block should contain ISIZE=0
IORDER contains the bond order for the bond between the current atom and the next atom in the block. For the last atom in the block, the bond order is for the bond between the last and first atoms in the block
CELEM must be an element symbol, not an atom type
Only the relative positions of the atoms in the ring are used by THINK
The order of the atoms in the ring definition is important. The priority is defined by the atomic number, followed by the degree of unsaturation. Thus, the ring definition should start with the heaviest heteroatom, and should proceed by the shortest path to the next heaviest heteroatom (if present) or unsaturated bond. If there are no heteroatoms then the definition should start with an unsaturated bond and proceed via that bond and the shortest path to the next unsaturated bond

A.5 Ring Torsion Angles

Data:

ISIZE, IORDER, CELEM, RTORS

Format:

2I3, 1X, A4, F9.3

Description:

ISIZE

Number of atoms in ring, or 0 for next ISIZE-1 records

IORDER

Bond order for bond between atoms n and n+1 in ring:
	1	single
	2	aromatic
	8	double
	16	triple

CELEM

Element for atom n

RTORS

F9.3

Torsion angle about bond between atoms n and n+1

The ring torsion angles parameter file is divided into blocks of records; each block defining one ring and containing one record per atom in the ring. A non-zero value of ISIZE indicates the beginning of a ring definition; all remaining records in that block should contain ISIZE=0
IORDER contains the bond order for the bond between the current atom and the next atom in the block. For the last atom in the block, the bond order is for the bond between the last and first atoms in the block
CELEM must be an element symbol, not an atom type
The atoms in the ring definition must be ordered in the same way as in a ring coordinates parameter file – see above

Appendix B