CONFLEX Keyword Options
In order to run a conformational search or a crystal structure search using CONFLEX, an initial settings file (.ini) containing the keywords for the settings must be created beforehand. When there is no .ini file, geometry optimization using the default MMFF94s force field is carried out.
When calculations are run from the CONFLEX Interface, an .ini file is generated automatically. If you want to specify the keywords other than on interface's dialogs, you can edit .ini file by hand.
The .ini file can be created using a text editor. Keywords (switches) and their descriptions are listed below.
Please note: If multiple options are designated for a keyword which requires only one option, inaccurate results may be generated.
Force Field Settings
Pseudo force of 5-membered ring phase angle is provided. When standard angle STD (°) is set to 360.0 or larger, the angle (°) of the initial structure is given as the defaults. And when force constants FK of harmonic potential function is set to zero, 1,000 (kcal/mol/rad^{2}) is given as the defaults.Keyword | Options | Description |
---|---|---|
EMM2 | Extended MM2 force field is used for calculation. | |
MM2 | MM2 force field is used for calculation. | |
MM3 | MM3(92) force field is used for calculation. | |
MMFF |
MMFF94 force field is used for calculation. | |
MMFF94S | MMFF94s force field is used for calculation. (Default) | |
DIELEC= | f.ff | Definition of the dielectric constant of the force field calculation employed. By default, this value is set to 1.0 for MMFF and 1.5 for MM2 and MM3. |
ELECSTAT= |
BCI |
The method of electrostatic calculation is changed. Although the electrostatic term is inherent in the force field (BCI for MMFF94 and MMFF94s, etc), user can select the other methods for the calculation. |
PSEUDO_BOND= | (I,J,STD,FK) | Pseudo force between I-th and J-th atoms is provided. When standard length STD and force constants FK of harmonic potential function are set to zero, the distance (angs.) of the initial structure and 10,000 (kcal/mol/Å^{2}), respectively are given as the defaults. |
PSEUDO_DIST= | (I,J,STD,FK) | Same as "PSEUDO_BOND=" above. |
PSEUDO_ANGL= | (I,J,K,STD,FK) | Pseudo force of I-J-K angle is provided. When standard angle STD (°) and force constants FK of harmonic potential function are set to zero, the angle (°) of the initial structure and 10,000 (kcal/mol/rad^{2}), respectively are given as the defaults. |
PSEUDO_TORS= | (I,J,K,L,STD,FK) | Pseudo force of I-J-K-L torsion angle is provided. When standard angle STD (°) is set to 360.0 or larger, the angle (°) of the initial structure is given as the defaults. And when force constants FK of harmonic potential function is set to zero, 1,000 (kcal/mol/rad^{2}) is given as the defaults. |
PSEUDO_OOPL= | (I,J,K,L,STD,FK) | Pseudo force of I=J-K(-L) out-of-plane angle is provided. When standard angle STD (°) is set to 360.0 or larger, the angle (°) of the initial structure is given as the defaults. And when force constants FK of harmonic potential function is set to zero, 1,000 (kcal/mol/rad^{2}) is given as the defaults. |
PSEUDO_PHI5= | (I,J,K,L,M,STD,FK) | |
PSEUDO_HALF= | (I,J,STD,FK) | Pseudo force of elongation between I-th and J-th atoms is provided. When standard distance STD（Å）and force constants FK of half harmonic potential function are set to zero, the distance (Å) of the initial structure and 10 (kcal/mol/Å^{2}), respectively are given as the defaults. |
PSEUDO_MORS= | (I,J,STD,FK,ALFA) | Pseudo force with Morse function is provided. When standard distance STD (Å) and force constants (dissociation energy) FK and direction factor ALFA are set to zero, the distance (Å) of the initial structure, 1,000 (kcal/mol/Å^2), and +1.0 (kcal/mol), respectively, are given as the defaults. |
SET_VELEC= | (I,J) | Temporary change the hybridization of the I-th atom into J value. Where I is a serial number of the atom that will be changed the number of valence electrons by user, and J is the number of valence electrons of the I-the atom. |
SET_CHARGE= | (dd,ff.ff) |
Set the atomic charge. For example, if you want to set the charge of atom 1 to 0.5, do the following SET_CHARGE=(1,0.5) |
Force Field Parameter Configure Keywords
Keyword | Options | Description |
---|---|---|
SET_ATOM_TYPE= | (IDX,ATYPE) | A numerical atom type for IDX-th atom is changed into ATYPE value. |
SET_EXT_ATOM_TYPE= | (IDX,ATYPE) |
A numerical atom type for IDX-th atom is set to ATYPE value. ATYPE value should be equal or larger than 900. |
STRETCH= *a) |
(I,J,BORDER,FK,STD) |
Bond stretching parameters between I-J are set. |
BEND= *a) |
(I,J,K,RING,FK,STD) |
Angle bending parameters for I-J-K are set. |
TORSION= *a) |
(I,J,K,L,BORDER,RING, |
Torsion interaction parameters for I-J-K-L are set. |
TORSION6= |
(I,J,K,L,BORDER,RING, |
Torsion interaction parameters up to 6th degree for I-J-K-L are set. |
OPLANE= *a) |
(I,J,K,L,FK) |
Out-of-plane bending parameter for I-J-K;L are set. |
STRBND= *a) |
(I,J,K,FK_IJ,FK_KJ) |
Stretch-bend interaction parameters for I-J-K are set. |
VDWATOM= *a) |
(I,DA,ALPHA,N,A,G) |
"Buffered-14-7" form van der Waals interaction parameters for I are set. |
FRMCHG= *a) |
(I,FC,CHARGE) |
Formal atomic charge for I are set. |
BNDCHG= *a) |
(I,J,BCI) |
Bond charge increment parameter for bond I-J are set. |
a) available for MMFF94s