Conformation Clustering Keyword
Keyword  Options  Description 

CLUSTER 
Conformation clustering will be performed by using a single linkage algorithm. This keyword should be used with “CONFLEX” keyword. 

CCLUS_DISTANCE=  Definition of conformation distance (similarity) to be used for conformation clustering.  
TORSION  RMS difference of torsion angles.  
ATOM  RMS difference of atomic position after superimposing.  
CCLUS_REFALL= 
Automatically defines the reference atoms or torsion angles to determine the conformation distance. When “CCLUS_DISTANCE=TORSION” is selected to the conformation distance 

TORSION  All torsion angles to be used.  
COMPAR  All torsion angles to be used for comparison with conformers.  
PHIPSI  All φ/ψ torsion angles of peptide. (only for peptide)  
When “CCLUS_DISTANCE=ATOM” is specified to the conformation distance, the following options can be specified: 

ALPHA  All α carbons of peptide (only for peptide)  
HEAVY  All heavy atoms  
NOHYD  All atoms except for hydrogen  
CCLUS_IREF= 
I 
The atom number of the referenced atom, or atom numbers of the central bond of the reference torsion angle. This keyword uses one line to specify one reference. 
CCLUS_XREF= 
I 
The atom number of the atom to be excluded from reference atoms, the atom numbers of the central bond to be excluded from reference torsion angles. This keyword uses one line to specify one reference. 
CCLUS_LIMIT= 
f.ff 
Threshold of conformation distance for conformation clustering AUTO prepares the threshold automatically 
CCLUS_LIMIT_MAX=  f.ff  Maximum value of threshold for conformation clustering 
CCLUS_EGFUNC=  Sort index is specified.  
STERIC  sorted by the “STERIC” energy order  
FREE  sorted by the Gibbs' “FREE” energy order  
CCLUS_MAXCONF=  n  Maximum number of conformers referenced in conformation clustering. 
UV/Vis/CD Spectrum and PPP/SCFMO keyword
Keyword  Options  Description 

UVCD  UV/Vis/CD Spectrum calculation will be performed.  
CDUV  Same with “UVCD”  
PIA_OPT=  In PPP/SCFMO calculation, all πatoms are automatically selected. However, SCF Instability is often caused by including some types of πatoms, carbonyl and peptide bonds in widely distributed aromatic system.  
NOPEP  exclude all peptide bonds (CONH)  
NOATE  exclude all carboxyl groups (COO)  
PIA_DEL=  I  Exclude Iatom from πatoms 
SCF=  Selection of SCF methods  
PPP  General PPP/SCFMO calculation  
VESCF  Variable electronegativity calculation (Allinger's approach)  
PPP=
Example: 
Extensions of SCFPPP calculation.  
VB  Variable beta method  
VG  Variable gamma method  
NEWG  New gamma method  
SCF_ITER=  N  Maximum number of SCF iterations. 
SCF_CONV=  f.ff  Threshold of SCF convergence. 
PPPATOM=  (I,J,Z,IP,G,H) 
Parameters of onecenter term for atom type I bonded to atom type J (I and J are atom type number of MM2 force field): 
PPPBOND=  (I,J,B,K,A_0,A_1) 
Parameters for bond between atom types I and J: 
PPPGAMM=  (I,J,D_0,D_1) 
Parameters for bond between atom types I and J: 
CIS=
Example: 
(Nomo,Numo)  Specifies the number of electrons on the occupied and unoccupied molecular orbitals consid ered in SingleCI calculation. 
CURVE_PLOT=  (f1,f2,f3) 
Range of spectrum, and incremental width for curvefitting based on the gauss approximation.

CURVE_DSIGMA=  f.ff 
Standard deviation of the Gaussian distribution. 
NMR Analysis Keyword
Keyword  Options  Description 

NMR 
NMR ^{3}J coupling constant calculation is performed. 

NMR_3J_ATYPE=  (W,X,Y,Z)(A)(COS,P_ COS,m,B1,B2,...) (SIN,P_ SIN,n,C1,C2,...) 
Parameters of Karplus equation for ^{3}J_{WZ} coupling constants around XY bond are set. The general formula of Karplus equation is as follows:
where W, X, Y, and Z are the serial number of atom types, and θ is WXYZ dihedral angle. Atom types, constants, and coefficients are separated by parentheses. the corresponding keyword is below: NMR_3J_ATYPE=(1,6,1,5)(1.0)(COS,15.0,2,2.0,3.0)(SIN,30.0,2,4.0,5.0) If the equation including only cosine as below is applied, the corresponding keyword is: NMR_3J_ATYPE=(1,6,1,5)(1.0)(COS,5.0,3,2.0,3.0,4.0) 
NMR_3J_NUNBER=  (I,J,K,L)(A)(COS,P_COS,m,B1,B2,...)(SIN,P_SIN,n,C1,C2,...) 
Parameters of Karplus equation for NMR ^{3}J_{IL} coupling constants around JK bond are set. The general formula of Karplus equation is same as above, I, J, K, and L are serial num bers of input data, and θ is IJKL dihedral angle. Serial numbers, constants, and coefficients are separated by parentheses.
Example: the corresponding keyword is below: NMR_3J_NUMBER=(1,2,3,4)(1.0)(COS,15.0,2,2.0,3.0)(SIN,30.0,2,4.0,5.0) If the equation including only cosine as below is applied, the corresponding keyword is below: NMR_3J_NUMBER=(1,2,3,4)(1.0)(COS,5.0,3,2.0,3.0,4.0) Note: When the parameters for IJKL are already set by the keyword “NMR_3J_ATYPE=”, the setting based on the atom types is overridden by this keyword. 
Solvent Effect Analysis Related Keywords using Generalized Born (GB/SA)
Keyword  Options  Description 

GBSA  GB/SA calculation will be performed.  
GBSA_ANALYZER= 
SINGLE 
Solvation energy analysis based on GB/SA calculation will be performed. In all options, GB/SA calculation will be performed after geometry optimization in gas phase. These options are set to the type of GB/SA calculation: singlepoint (SINGLE) geometry optimization (OPTIMZ or FREE) Solvation energy is defined by the total energy difference between gas phase and in solvent (SINGLE and OPTIMZ) or defined by the free energy difference between gas phase and in solvent (FREE). 
GBSA_SOLVENT= 
WATER 
Solvent type is specified. If no solvent name, water environment will be applied as default. 
MOL_DIELEC=  f.ff 
Define the dielectric constant of molecule. By default, this value is set to 1.0. 
SA=  NUM  The calculation of solvent accessible surface area will be performed numerically. 
IGNORE  Do not calculate the nonelectrostatic term.  
NLR= 
ON 
NeighborList Reduction will be performed. 
INIT_GEOM=  SAME  Initial geometry for the calculation that is including solvent effect is set to same as input geometry. 