CONFLEX Manual

Constraint Driving Keywords

Keyword	Options	Description
CONSTR_BOND= CONSTR_DIST=	(I,J,STA,TER,STP,FK)	Constraint of distance between I-th and J-th atoms (not necessary bonded) is provided. STA: Start Length (Å) TER: Termination Length (Å) STP: Driving Step Size (Å) FK: Force Constant (Default: 10,000 kcal/mol/Å²) When start length STA, termination length TER, driving step size STP (Angs) are given appropriately, force constants FK of constraint function is automatically set to 10,000 (kcal/mol/Å²), and then stepwise structural modification along the speci- fied reaction coordinate (I-J distance) will be performed with constraint optimization.
CONSTR_ANGL=	(I,J,K,STA,TER,STP,FK)	Constraint of I-J-K angle (not necessary bonded) is provided. FK is set to 10,000 (kcal/ mol/rad²) as default. When STA, TER, STP angles (°) are given appropriately, structural modification will be performed with constraint optimization. STA: Start Angle (°) TER: Termination Angle (°) STP: Step Size (°) FK: Force Constant (Default: 10,000 (kcal/mol/rad²)
CONSTR_TORS=	(I,J,K,L,STA,TER,STP,FK)	Constraint of I-J–K-L torsion (dihedral) angle (not necessary bonded) is provided. STA: Start Angle (°) TER: Termination Angle (°) STP: Step Size (°) FK: Force Constant (Default: 1,000 (kcal/mol/rad²)
CONSTR_OOPL=	(I,J,K,L,STA,TER,STP,FK)	Constraint of out-of-plane angle of I-J-K plane (not necessary bonded) and L-th atom is provided. FK is set to 1,000 (kcal/mol/rad2) as default. STA: Start Angle (°) TER: Termination Angle (°) STP: Step Size (°) FK: Force Constant (Default: 1,000 (kcal/mol/rad²)
CONSTR_PHI5=	(I,J,K,L,M,STA,TER,STP,FK)	5-membered ring phase angle is provided. STA: Start Angle (°) TER: Termination Angle (°) STP: Step Size (°) FK: Force Constant (Default: 1,000 (kcal/mol/rad²)

Stochastic Kick Keyword

Keyword	Options	Description
KICK		Stochastic Kick method will be applied as a pre-perturbation before the specified optimization. The random seed number is set to the constant“123456789” as default.
KICK=	n	Constant of the random seed number is specified to n.
KICK_RESET		The random seed number will be changed in each call of random generation. The initial seed number is set to the default number.
KICK_RESET=	n	The random seed number will be changed in each call of random generation. The initial seed number is set to n.
KICK_FACTOR=	f	Size of stochastic kick vector is set to 0.01 Åas the default. If the kick factor ‘f’ is specified, the maximum kick size will be set to 0.01*f Å.

Dynamic Reaction Coordinate (DRC) Keyword

Keyword	Options	Description
DRC		DRC calculation will be performed.
DRC_SMODE=	n	Specify one normal mode used for DRC calculation. Default value is 1.
DRC_MMODE=	n1,n2	Specify range of multiple normal modes used for DRC calculation. These are mixed between n1 through n2.
DRC_NSTEP=	ff.ff	Set the time step (unit in ps). Default value is 0.0002.
DRC_TERMN=	ff.ff	Set the termination time (unit in ps). Default value is 4/(ν_i*c), where ν_i is vibrational frequency of the lowest normal mode among the selected modes and c is the speed of light.
DRC_TEMP=	ff.ff	Set temperature (°C) for DRC calculation. Default value is 25.0.(°C)
DRC_SCALE=	ff.ff	Set scaling factor for amplitude of selected normal mode(s). Default value is calculated from sum of the vibrational frequencies of selected normal modes and the sum of the kinetic energies.
DRC_KICK=	ff.ff	Set value (unit in kcal/mol) for scaling factor instead of sum of the frequencies.
DRC_PHASE=	(ff.ff,...)	Set phase angle (unit in degree) for each normal mode. Default value is -90.
SNAPSHOT=	n	Output the coordinate data every n steps. Default value is 100.

invoking External Program (Gaussian 09 or 16) Keywords

Keyword	Options	Description
EXTERNAL_PROGRAM=	GAUSSIAN	Set external program for calculation.
EXT_GAU_ROUTE=	(“...”)	Specify the route section of Gaussian. Example: EXT_GAU_ROUTE=("opt hf/3-21g")
EXT_GAU_LINK0=	(“...”)	Specify the Link0 commands of Gaussian (possible to set multiple). Example: EXT_GAU_LINK0=(NprocShared=2)
EXT_GAU_COMMENT=	(“...”)	Specify the comment line of Gaussian input file. Example: EXT_GAU_COMMENT=("Gaussian invoked by CONFLEX")
EXT_GAU_CHARGE=	n	Set charge value of molecule.
EXT_GAU_SPIN=	n	Set spin multiplicity of molecule.
EXT_GAU_HEADER_FILE=	filename	Specify the file name that is including the description above coordinate specification (Link0 commands, route section, comment, charge and spin multiplicity).
EXT_GAU_FOOTER_FILE=	filename	Specify the file name that is including the description below coordinate specification (basis set, solvent effect, etc.).
EXT_PREOPT= Default: ON	ON OFF	Set whether geometry optimization using force field is executed before invoking external program.
EXT_GAU_SCRDIR= Windows only	Directory Path	Specify the scratch directory that is the location of output and scratch files. Default is “%GAUSS_EXEDIR%\Scratch”.
EXT_JOB_COM=	(“...”)	Specify the run command for executing with shell script or job scheduler. Note that the option for interactive job must be including in the run command when the job scheduler is used. Example: Grid Engine: “qsub -sync yes” Platform LSF: “bsub -K <”
EXT_JOB_FILE=	filename	Specify the setting file name that describes the settings to be read by the shell script or job scheduler.

Other Keywords

Keyword	Options	Description
FILE_TYPE= Default: MOL	MOL MOL2 PDB CIF CMF	Choose the type of input file format (extension: .mol, .mol2, .pdb, .cif, or .cmf ).
TIME= Example: TIME=10.00D	f.ff	The total CPU time allowed for the current job is limited to f.ff seconds (default). Alternative specifications of the time are T=f.ff D, T=f.ff H, T=f.ff M, which define the time in ff.ff days, hours, minutes, respectively. If this TIME keyword is not used, default time limit is 3 days (=259,200 seconds).
DEBUG		Specification of “DEBUG” keyword provides debugging information for all subroutines. “DEBUG” keyword is corresponding to “DEBUG=ALL”, see below.
DEBUG=	CONCHK HYBRID DEFINE CLASSALL CLASS[0-8] CLASSPPP SYMM EVAL OPT SCFMO ALL	Debugging information can be provided for the following subroutines: CONCHK, HYBRID, DEFINE, CLASSALL, CLASS[0-8], CLASSPPP, SYMM, EVAL, OPT, ALL, NEWTON. Example : DEBUG=(CONCHK,SYMM)
PRINT= NOPRINT=	INPUT MODE LATEST PARAM SYMM NEGEIG SCFMO	Options are used to specify what information should (or should not) be output.