CONFLEX Tutorials

Customize force field parameters

A molecular force field provides force field parameters necessary for evaluating various interactions. If the parameters required to calculate a target molecule are not available in the force field, the molecule cannot be calculated. This section explains how to add missing parameters and how to modify the parameters of force field in used. Calculations for the metal complex [Ti(H2O)6]3+ and acetic acid CH3COOH are shown below as example.

* Metal complex [Ti(H2O)6]3+

Input structure and its data of [Ti(H2O)6]3+ are shown below. CONFLEX cannot perform any calculations on the structure due to the lack of force field parameters for Ti3+.

Input structure of [Ti(H2O)6]3+

Ti(H2O)6 3+

Structure data (Ti3+H2O6.mol)

Ti3+H2O6.mol


19 12  0  0  0  0  0  0  0  0  0    0
    0.7679   -0.0417    0.0000 Ti  0  1  0  0  0  0  0  0  0  0  0  0
    0.7679    1.9383    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1801    2.4183    0.5879 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7479   -0.0417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.2279   -0.8728   -0.0216 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7679   -0.0417    1.9800 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1899   -0.6393    2.4600 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7679   -2.0217    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1945   -2.5017   -0.6020 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2121   -0.0417    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6921    0.0066   -0.8300 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7679   -0.0417   -1.9800 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3468    0.5551   -2.4600 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1891   -0.6385   -2.4600 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3558    2.4183   -0.5879 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3414   -2.5017    0.6020 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2279    0.7894    0.0216 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3460    0.5558    2.4600 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6921   -0.0901    0.8300 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  3  1  0  0  0  0
  2 15  1  0  0  0  0
  4  5  1  0  0  0  0
  4 17  1  0  0  0  0
  6  7  1  0  0  0  0
  6 18  1  0  0  0  0
  8  9  1  0  0  0  0
  8 16  1  0  0  0  0
 10 11  1  0  0  0  0
 10 19  1  0  0  0  0
 12 13  1  0  0  0  0
 12 14  1  0  0  0  0
M  END

[Execution from Interface]

Open the Ti3+H2O6.mol file using CONFLEX Interface.

Interface Ti3+(H2O)6

Select [CONFLEX] from the Calculation menu, and then click Detail Settings in the calculation setting dialog that appears. Next, click Edit & Submit at the bottom right in the detailed settings dialog.

Add keywords of [SET_EXT_ATOM_TYPE=(1,900)], [VDWATOM=(900,-,0.45,6.0,4.0,1.4)], and [FRMCHG=(900,3,3.0)] to the dialog that appears.

Interface Edit Submit

The [SET_EXT_ATOM_TYPE=(1,900)] sets the atom type of Ti3+ with serial number of 1 to 900.
The [VDWATOM=(900,-,0.45,6.0,4.0,1.4] sets the van der Waals interaction parameter for the atom with atom type 900.
The [FRMCHG=(900,3,3.0)] sets the formal charge of the atom with atom type 900 to +3 and its partial charge to +3.0, respectively.

After completing the calculation settings, click Submit to start the calculation.

[Execution from command line]

The calculation settings are defined by specifying keywords in the Ti3+H2O6.ini file.

Ti3+H2O6.ini file

MMFF94S
SET_EXT_ATOM_TYPE=(1,900)
VDWATOM=(900,-,0.45,6.0,4.0,1.4)
FRMCHG=(900,3,3.0)

The [SET_EXT_ATOM_TYPE=(1,900)] sets the atom type of Ti3+ with serial number of 1 to 900.
The [VDWATOM=(900,-,0.45,6.0,4.0,1.4] sets the van der Waals interaction parameter for the atom with atom type 900.
The [FRMCHG=(900,3,3.0)] sets the formal charge of the atom with atom type 900 to +3 and its partial charge to +3.0, respectively.

Store the Ti3+H2O6.mol and Ti3+H2O6.ini files in a single folder, and execute the following command to start the calculation. 

C:\CONFLEX\bin\conflex-10a.exe   -par   C:\CONFLEX\par   Ti3+H2O6
enter

The command above is for Windows OS. For other OS, please refer to [How to execute CONFLEX].

Calculation results

The optimized structure is shown below. For how to visualize this, please refer to [Visualization of calculation results].

Optimized structure of [Ti(H2O)6]3+

Ti(H2O)6 opt

Structure data (Ti3+H2O6-F.mol)

Ti3+H2O6-F.mol
CONFLEX 14011413263D 1   1.00000  -477.60875     0
TH  ,E = -477.609, G = 2.324E-07, M(0)      MMFF94S(2010-12-04HG)
 19 12  0     0                 0 V2000
   -0.0000    0.0000    0.0000 Ti  0  1  0  0  0
    1.1603    0.8140    1.4174 O   0  0  0  0  0
    1.9869    1.3938    1.4008 H   0  0  0  0  0
   -1.1603   -0.8140    1.4174 O   0  0  0  0  0
   -1.1501   -1.6932    1.9140 H   0  0  0  0  0
   -1.1511    1.6410    0.0000 O   0  0  0  0  0
   -1.9745    1.9212   -0.5131 H   0  0  0  0  0
   -1.1603   -0.8140   -1.4174 O   0  0  0  0  0
   -1.1468   -0.8045   -2.4271 H   0  0  0  0  0
    1.1603    0.8140   -1.4174 O   0  0  0  0  0
    1.9836    0.5051   -1.9140 H   0  0  0  0  0
    1.1511   -1.6410   -0.0000 O   0  0  0  0  0
    1.9745   -1.9212    0.5131 H   0  0  0  0  0
    1.1344   -2.5106   -0.5131 H   0  0  0  0  0
    1.1468    0.8045    2.4271 H   0  0  0  0  0
   -1.9869   -1.3938   -1.4008 H   0  0  0  0  0
   -1.9836   -0.5051    1.9140 H   0  0  0  0  0
   -1.1344    2.5106    0.5131 H   0  0  0  0  0
    1.1501    1.6932   -1.9140 H   0  0  0  0  0
  2  3  1  0     0
  2 15  1  0     0  
  4  5  1  0     0
  4 17  1  0     0
  6  7  1  0     0
  6 18  1  0     0
  8  9  1  0     0
  8 16  1  0     0
 10 11  1  0     0
 10 19  1  0     0
 12 13  1  0     0
 12 14  1  0     0
M  END

* Acetic acid CH3COOH

Input structure and its data of CH3COOH are shown below.

Input structure of CH3COOH

CH3COOH inp

Structure data (CH3COOH.mol)

CH3COOH.mol


  8  7  0  0  0  0  0  0  0  0  0    0
    0.1268    0.0794    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1528    0.7584    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0615    0.7347    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9219    1.6958    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0496   -1.4504    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5898   -1.7472    0.8747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5898   -1.7472   -0.8747 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9117   -1.9203    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  1  3  1  0  0  0  0
  1  5  1  0  0  0  0
  3  4  1  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5  8  1  0  0  0  0
M  END

The force field parameters for CH3COOH molecule are included in the force field provided by CONFLEX. However, you can modify these parameters using keywords.

[Execution from Interface]

Open the CH3COOH.mol file using CONFLEX Interface.

Interface CH3COOH

Select [CONFLEX] from the Calculation menu, and then click Detail Settings in the calculation setting dialog that appears. Next, click Edit & Submit at the bottom right in the detailed settings dialog.

Add keywords for setting the force field parameters to the dialog that appears. About explanations of the keywords, please refer to the manual.

Interface Edit Submit

After completing the calculation settings, click Submit to start the calculation.

[Execution from command line]

Add keywords for setting the force field parameters to the CH3COOH.ini file. About explanations of the keywords, please refer to the manual.

CH3COOH.ini file

MMFF94S
SET_EXT_ATOM_TYPE=(1,903)
SET_EXT_ATOM_TYPE=(2,907)
SET_EXT_ATOM_TYPE=(3,906)
SET_EXT_ATOM_TYPE=(4,924)
SET_EXT_ATOM_TYPE=(5,901)
SET_EXT_ATOM_TYPE=(6,905)
SET_EXT_ATOM_TYPE=(7,905)
SET_EXT_ATOM_TYPE=(8,905)
STRETCH=(901,903,1,4.190,1.492)
STRETCH=(901,905,1,4.766,1.093)
STRETCH=(903,906,1,5.801,1.355)
STRETCH=(903,907,2,12.950,1.222)
STRETCH=(906,924,1,7.403,0.981)
BEND=(903,901,905,0,0.650,108.385)
BEND=(905,901,905,0,0.516,108.836)
BEND=(901,903,906,0,1.043,109.716)
BEND=(901,903,907,0,0.938,124.410)
BEND=(906,903,907,0,1.155,124.425)
BEND=(903,906,924,0,0.583,111.948)
TORSION=(905,901,903,906,0,6,0.0,0.624,0.330)
TORSION=(905,901,903,907,0,6,0.659,1.407,0.308)
TORSION=(901,903,906,924,0,6,-1.166,-5.078,-0.545)
TORSION=(907,903,906,924,0,6,1.662,-6.152,-0.058)
OPLANE=(901,903,906,907,0.141)
STRBND=(903,901,905,0.157,0.115)
STRBND=(905,901,905,0.115,0.115)
STRBND=(901,903,906,0.338,0.732)
STRBND=(901,903,907,0.154,0.856)
STRBND=(906,903,907,0.494,0.578)
STRBND=(903,906,924,0.215,0.064)
VDWATOM=(901,-,1.05,2.49,3.89,1.282)
VDWATOM=(903,-,1.10,2.49,3.89,1.282)
VDWATOM=(905,-,0.25,0.80,4.20,1.209)
VDWATOM=(906,A,0.70,3.15,3.89,1.282)
VDWATOM=(907,A,0.65,3.15,3.89,1.282)
VDWATOM=(924,D,0.15,0.80,4.20,1.209)
BNDCHG=(901,903,-0.061)
BNDCHG=(903,906,-0.15)
BNDCHG=(903,907,-0.57)
BNDCHG=(906,924,0.50)

Store the CH3COOH.mol and CH3COOHl.ini files in a single folder, and execute the following command to start the calculation. 

C:\CONFLEX\bin\conflex-10a.exe   -par   C:\CONFLEX\par   CH3COOH
enter

The command above is for Windows OS. For other OS, please refer to [How to execute CONFLEX].