Conformation search
This section explains how to execute a conformation search by CONFLEX.
“Cyclohexane-F.mol” file obtained in the “Execution of structure optimization and vibrational analysis” is used as a structure file. The Cyclohexane-F.mol has data of the optimized structure of Cyclohexane.
[Execution of conformation search]
[Execution by Interface]
Open the Cyclohexane-F.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and select [Conformation Search] in the pull-down menu of [Calculation Type:] on the calculation setting dialog displayed.
Leave the value of [Search Limit:] at 1.0. This parameter is used as a criteria for selecting initial structure in the conformation search. In the calculation, conformers found in a region within 1.0 kcal/mol from the most stable conformer are selected as initial structure. Therefore, when the calculation is finished, it is considered that the conformation search on the energy region (within 1.0 kcal/mol) is complete.
When the calculation settings are complete, click . The calculation will start.
[Execution by command line]
The calculation settings are defined by describing keywords in the Cyclohexane-F.ini file.
Cyclohexane-F.ini file
MMFF94S CONFLEX SEARCH=ENERGY SEL=1.0
Explanations of each keyword are shown below.
- MMFF94S
- Use MMFF94s
- CONFLEX
- Execute a conformation search
- SEARCH=ENERGY
- Search limit on conformational space is determined by energy.
- SEL=1.0
- The search limit sets to 1.0 kcal/mol.
The search limit is used as a criteria for selecting initial structure in the conformation search. In the calculation, conformers found in a region within 1.0 kcal/mol from the most stable conformer are selected as initial structure. Therefore, when the calculation is finished, it is considered that the conformation search on the energy region (within 1.0 kcal/mol) is complete.
The settings by the keywords of “MMFF94S”, “SEARCH=ENERGY”, and “SEL=1.0” equal to default them. Therefor, even if you use the following ini file, the settings in both the calculations will match.
Cyclohexane-F.ini file
CONFLEX
Store the two files of Cyclohexane-F.mol and Cyclohexane-F.ini in an one folder, and execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par Cyclohexane-Fenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
[Output files]
Three files of -F.mol, sdf, and bso files, that is, Cyclohexane-F-F.mol, Cyclohexane-F.sdf, and Cyclohexane-F.bso are outputted as in case of the structure optimization calculation.
Additionally, in case of the conformation search, the following files are also outputted.
- Cyclohexane-F.fxf
- This file has structure data of conformers found by the conformation search. If you restart the conformation search by using this file, you can only explore an extended conformational space from the previous result.
- Cyclohexane-F.fxo
- This file has a detail information on the conformation search including definition on local perturbation by flip-flap and corner flap, relation between conformers found, and so on.
- Cyclohexane-F.ls1
- The conformers found by the search are listed in order of steric energy in this file.
- Cyclohexane-F.ls2
- This file shows values of dihedral angles which are used in comparing conformers to check duplicates in the search.
- Cyclohexane-F.ls3
- This file shows data of CONF. ID, steric energy, distribution based on steric energy, atomic coordinates, and atom list of each conformer found by the search.
- Cyclohexane-F.ls4
- The conformers found by the search are listed in order of free energy in this file.
- Cyclohexane-F.sdf
-
Structure data of each conformer found by the search are stored in this file in MDL-MOL format.
A explanation of the MDL-MOL format is shown in Explanation about Cyclohexane.mol file.While there is one structure data in the MOL file, more than one structure data can be described in the SDF file by separating them with “$$$$”. Therefor, if you divide structure data in the SDF file by $$$$, you can get the MOL file of each structure. The order of structure data in the SDF file is according to total Gibbs's free energy. Each structure data is identified by “IFN=”, and the first number is Gibbs's free energy rank, and the second number is unique conformer ID in the search.
0.7343750
18
2
1.00000000000000
5.200
1
T
F
0
F
6
D3D
-3.56093559779315
3.249848646468316E-009
0.888728442903559 1.48121407150593 39.2016730029237
-10.2067647343158 4.96801633911096 0.888728442903559
0.888728442903559 22.7814526607543 -5.90356166790034
2.98080980346657 106.763590387419 106.763590387419
8.44981392719261 104.244278365026 16.4665174320397
-3.56093559779315 -3.56093559779315 0.000000000000000E+000
-3.56093559779315 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 0.000000000000000E+000 0.000000000000000E+000
0.000000000000000E+000 104.980111675433 105.572597304035
70.4329395908707 84.5730163650170 24.4153435746172
105.050542904982 13.6944155520592 0.000000000000000E+000
56.7385240388114 6.00000000000000
116.679654042328 116.679654042695 204.596311457385
0.000000000000000E+000 0.000000000000000E+000
***** START LOOP OF CONFLEX SEARCH ***** 18 TRIAL STRUCUTRES GENERATED FROM 1 INITIAL STRUCTURE(S). COUNT OF STACKED INITIAL STRUCUTRES: 1 INITIAL STRUCTURE - IDN: 1, EGY: -3.5609 NUMBER OF TRIAL CONFORMATIONS GENERATED: 18 NUMBER OF INITIAL STRUCTURES LEFT: 1 A NEW CONFORMER - IFT: 21,IDN: 2, EGY: 2.3688, GRMS: 0.81E-07, TIME: 0.05 REPLACED OLD ONE - IFT: 22,IDN: 2, EGY: 2.3688, GRMS: 0.50E-08, TIME: 0.03 IDENTICAL OLD ONE - IFT: 23,IDN: 2, EGY: 2.3688, GRMS: 0.74E-07, TIME: 0.03 REPLACED OLD ONE - IFT: 24,IDN: 2, EGY: 2.3688, GRMS: 0.98E-07, TIME: 0.05 IDENTICAL OLD ONE - IFT: 25,IDN: 2, EGY: 2.3688, GRMS: 0.64E-06, TIME: 0.03 IDENTICAL OLD ONE - IFT: 26,IDN: 2, EGY: 2.3688, GRMS: 0.17E-07, TIME: 0.05 IDENTICAL OLD ONE - IFT: 10,IDN: 2, EGY: 2.3688, GRMS: 0.14E-06, TIME: 0.03 REPLACED OLD ONE - IFT: 20,IDN: 1, EGY: -3.5609, GRMS: 0.32E-08, TIME: 0.03 REPLACED OLD ONE - IFT: 10,IDN: 2, EGY: 2.3688, GRMS: 0.20E-07, TIME: 0.05 IDENTICAL OLD ONE - IFT: 20,IDN: 1, EGY: -3.5609, GRMS: 0.14E-07, TIME: 0.05 IDENTICAL OLD ONE - IFT: 10,IDN: 2, EGY: 2.3688, GRMS: 0.73E-07, TIME: 0.03 IDENTICAL OLD ONE - IFT: 20,IDN: 1, EGY: -3.5609, GRMS: 0.14E-07, TIME: 0.05 IDENTICAL OLD ONE - IFT: 10,IDN: 2, EGY: 2.3688, GRMS: 0.17E-08, TIME: 0.03 IDENTICAL OLD ONE - IFT: 20,IDN: 1, EGY: -3.5609, GRMS: 0.11E-06, TIME: 0.03 IDENTICAL OLD ONE - IFT: 10,IDN: 2, EGY: 2.3688, GRMS: 0.37E-08, TIME: 0.03 IDENTICAL OLD ONE - IFT: 20,IDN: 1, EGY: -3.5609, GRMS: 0.15E-08, TIME: 0.08 IDENTICAL OLD ONE - IFT: 10,IDN: 2, EGY: 2.3688, GRMS: 0.26E-09, TIME: 0.03 IDENTICAL OLD ONE - IFT: 20,IDN: 1, EGY:
!====================================================================================!
! !
! LIST OF CONFORMERS (LIST FORM 1) !
! !
!------------------------------------------------------------------------------------!
! !
! DATE: 2020/09/04 TIME: 16:04:19.46 !
! Cyclohexane-F: Cyclohexane.mol !
! EMPIRICAL FORMULA: C6H12 MW = 84.094 !
! FORCE FIELD: MMFF94S(2010-12-04HG) !
! TOTAL NUMBER OF CONFORMERS FOUND: 2 !
! STERIC ENERGY: MIN= -3.5609 MAX= 2.3688 AVERAGE= -3.5607 !
! !
!------------------------------------------------------------------------------------!
! !
! DEFINITIONS: !
! NO. = INDEX NUMBER IN THE ORDER OF STERIC ENERGY !
! CONF. ID = IDENTIFICATION NUMBER OF EACH CONFORMER !
! STERIC E = STERIC ENERGY OF EACH CONFORMER (KCAL/MOL) !
! DELTA E = RELATIVE STERIC ENERGY FROM THE GLOBAL ENERGY MINIMUM (KCAL/MOL) !
! DISTRIBUTION = DISTRIBUTION BASED ON STERIC ENERGY (%) !
! INIT. = FLAG OF THE INITIAL STRUCTURE THAT HAD BEEN ALREADY USED !
! "*" = INDICATES THE INITIAL STRUCTURE USED IN THIS JOB !
! REOPT. = FLAG OF THE OPTIMIZED STRUCTURE THAT HAD BEEN OPTIMIZED AGAIN !
! "+" = INDICATES THE NEW CONFORMERS FOUND IN THIS JOB !
! NO. NEG. = NUMBER OF NEGATIVE EIGEN VALUES OF EACH CONFORMER !
! !
!====================================================================================!
====================================================================================
CONF. ORIGINAL DISTRI- NO.
NO. ID STERIC E DELTA E BUTION INIT. REOPT. NEG.
------------------------------------------------------------------------------------
1 00000001 -3.5609 0.0000 99.9955 T* F+ 0
2 00000002 2.3688 5.9297 0.0045 F F+ 0
------------------------------------------------------------------------------------
MINIMUM ENERGY: -3.5609 KCAL/MOL
AVERAGE ENERGY: -3.5607 KCAL/MOL (BASED ON THE BOLTZMANN LAW)
====================================================================================
Explanations of each item are shown below.
| Item | Explanation |
|---|---|
| NO. | Number in order of steric energy |
| CONF.ID | Number assigned in order found by the search |
| ORIGINAL STERIC E | Steric energy (kcal/mol) |
| DELTA E | Relative steric energy from the lowest one (kcal/mol) |
| DISTRIBUTION | Conformation distribution obtained by Boltzmann distribution based on the steric energy |
| INIT. | Flag indicating whether it was used as an initial structure |
| REOPT. | Flag indicating whether it has already been subjected to a structure optimization or the search performed the structure optimization of it |
| NO. NEG. | The number of negative eigenvalues obtained by a normal mode analysis |
The value of INIT. for a conformer that was used as initial structure in the search shows “T” and “*”. The “T” means that the conformer has already been used in the search regardless of initial search or restart, and the “*” means that the conformer was used in the search that outputted the currently referred ls1 file.
State on structure optimization for a conformer indicates by “F” and “+”. The “F” means that the conformer has already been optimized. The “+” means that the conformer was optimized and newly found in the search that outputted the currently referred ls1 file.
In “NO. NEG”, “0” is shown if all eigenvalues are positive in the normal mode analysis of a conformer, and the number of negative eigenvalues is shown if the conformer has any negative eigenvalues.
When one eigenvalue shows negative, the structure is considered to be a transition state connecting between equilibrium conformers.
For a validation of the result in the force field calculation, it is recommended that you perform optimization, normal mode analysis and inherent reaction coordinate calculation of the structure by ab initio method in order to check it is the transition state or not.
!------------------------------------------------------------------------------------!
! !
! DEFINITIONS OF TORSION ANGLES: !
! D 1 = 3 - 1 - 2 - 16 !
! D 2 = 1 - 2 - 16 - 13 !
! D 3 = 2 - 16 - 13 - 8 !
! D 4 = 16 - 13 - 8 - 3 !
! D 5 = 13 - 8 - 3 - 1 !
! D 6 = 8 - 3 - 1 - 2 !
! !
!====================================================================================!
============================================================================================================
NO. ID STERIC E DELTA E DISTRIB. D 1 D 2 D 3 D 4 D 5 D 6
------------------------------------------------------------------------------------------------------------
1 00000001 -3.5609 0.0000 99.9955 -54.26 54.26 -54.26 54.26 -54.26 54.26
2 00000002 2.3688 5.9297 0.0045 29.17 29.17 -60.11 29.17 29.17 -60.11
------------------------------------------------------------------------------------------------------------
AVERAGE: -3.5607 0.0003
============================================================================================================
00000001 E= -3.5609; P= 99.9955 18 120. -1.26267 0.72901 0.22578 1 -0.00000 1.45801 -0.22578 1 -1.26267 -0.72901 -0.22578 1 -2.14619 1.23910 -0.17419 5 -1.33651 0.77163 1.31946 5 0.00000 2.47821 0.17419 5 -0.00000 1.54327 -1.31946 5 -0.00000 -1.45801 0.22578 1 -2.14619 -1.23910 0.17419 5 -1.33651 -0.77163 -1.31946 5 -0.00000 -2.47821 -0.17419 5 -0.00000 -1.54327 1.31946 5 1.26267 -0.72901 -0.22578 1 2.14619 -1.23910 0.17419 5 1.33651 -0.77163 -1.31946 5 1.26267 0.72901 0.22578 1 1.33651 0.77163 1.31946 5 2.14619 1.23910 -0.17419 5 STERIC E.= -3.56094 T F 00000002 E= 2.3688; P= 0.0045 18 120. -0.67151 1.22910 0.35868 1 -1.50939 0.00000 0.00000 1 0.67151 1.22910 -0.35868 1 -0.49926 1.24725 1.44233 5 -1.23203 2.13933 0.11739 5 -2.16866 0.23360 -0.84486 5 -2.16866 -0.23360 0.84486 5 1.50939 -0.00000 0.00000 1 0.49926 1.24725 -1.44233 5 1.23203 2.13933 -0.11739 5 2.16866 0.23360 0.84486 5 2.16866 -0.23360 -0.84486 5 0.67151 -1.22910 0.35868 1 1.23203 -2.13933 0.11739 5 0.49926 -1.24725 1.44233 5 -0.67151 -1.22910 -0.35868 1 -0.49926 -1.24725 -1.44233 5 -1.23203 -2.13933 -0.11739 5 STERIC E.= 2.36879 F F
!====================================================================================!
! !
! LIST OF CONFORMERS (LIST FORM 4) !
! !
!------------------------------------------------------------------------------------!
! !
! DATE: 2020/09/04 TIME: 16:04:19.46 !
! Cyclohexane-F: Cyclohexane.mol !
! EMPIRICAL FORMULA: C6H12 MW = 84.094 !
! FORCE FIELD: MMFF94S(2010-12-04HG) !
! TOTAL NUMBER OF CONFORMERS FOUND: 2 !
! STERIC ENERGY: EMIN= -3.5609 EMAX= 2.3688 EAVE= -3.5607 !
! GIBB'S FREE ENERGY: GMIN= 84.5730 GMAX= 88.7989 GAVE= 84.5764 !
! MIXING ENERGIES: HMIX= 105.5770 TSMIX= 21.0044 GMIX= 84.5725 !
! MIXING HEAT CAPACITY: CPMIX= 24.4158 !
! TEMPERATURE: 25.00 CELSIUS ( 298.15 KELVIN) !
! !
!------------------------------------------------------------------------------------!
! !
! DEFINITIONS: !
! NO. = INDEX NUMBER IN THE ORDER OF THE TOTAL GIBBS'S FREE ENERGY !
! CONF. ID = IDENTIFICATION NUMBER OF EACH CONFORMER !
! HE = ENTHALPY CONTRIBUTION OF EACH CONFORMER (KCAL/MOL) !
! TSE = ENTROPY (MULRPLIED BY TEMP.) CONTRIBUTION OF EACH CONFORMER (KCAL/MOL)!
! GE = TOTAL GIBB'S FREE ENERGY OF EACH CONFORMER (KCAL/MOL) !
! DGE = RELATIVE GIBB'S FREE ENERGY OF EACH CONFORMER (KCAL/MOL) !
! GEPOP = DISTRIBUTION IN GIBB'S FREE ENERGY (%) !
! SE = STERIC ENERGY OF EACH CONFORMER (KCAL/MOL) !
! DSE = RELATIVE STERIC ENERGY FROM THE GLOBAL ENERGY MINIMUM (KCAL/MOL) !
! SEPOP = DISTRIBUTION BASED ON STERIC ENERGY (%) !
! CHIRAL = CHIRALITY EXISTANCE OF EACH CONFORMER !
! SYM. NUM. = SYMMETRY NUMBER OF EACH CONFORMER !
! POINT GROUP = POINT GROUP OF SYMMETRY OF EACH CONFORMER !
! INIT. = FLAG OF EACH CONFORMER THAT HAD USED FOR INITIAL STRUCTURE !
! REOPT. = FLAG OF EACH CONFORMER THAT HAD BEEN OPTIMIZED AGAIN !
! NO. NEG. = NUMBER OF NEGATIVE EIGEN VALUES OF EACH CONFORMER !
! !
!====================================================================================!
========================================================================================================================================
CONF. SYM. POINT NO.
NO. ID HE TSE GE DGE GPOP SE DSE EPOP CHIRAL NUM. GROUP INIT. REOPT. NEG.
----------------------------------------------------------------------------------------------------------------------------------------
1 00000001 105.5726 20.9996 84.5730 0.0000 99.9202 -3.5609 0.0000 99.9955 F 6 D3D T F 0
2 00000002 111.0426 22.2436 88.7989 4.2259 0.0798 2.3688 5.9297 0.0045 T 4 D2 F F 0
----------------------------------------------------------------------------------------------------------------------------------------
========================================================================================================================================
Explanations of each item are shown below.
| Item | Explanation |
|---|---|
| NO. | Number in order of total Gibbs's free energy |
| CONF.ID | Number assigned in order found by the search |
| HE | Enthalpy (kcal/mol) |
| TSE | Entropy multiplied by temperature (kcal/mol) |
| GE | Total Gibbs's free energy (kcal/mol) |
| DGE | Relative Gibbs's free energy form the lowest one (kcal/mol) |
| GPOP | Conformation distribution obtained by Boltzmann distribution based on Gibbs's free energy |
| SE | Steric energy (kcal/mol) |
| DSE | Relative steric energy from the lowest one (kcal/mol) |
| EPOP | Conformation distribution obtained by Boltzmann distribution based on steric energy |
| CHIRAL | Flag indicating the conformer has chirality or not. |
| SYM. NUM. | Symmetry number |
| POINT GROUP | Symbol of point group |
| INIT. | Flag indicating whether it was used as an initial structure |
| REOPT. | Flag indicating whether it has already been subjected to a structure optimization or the search performed the structure optimization of it |
| NO. NEG. | The number of negative eigenvalues obtained by a normal mode analysis |
Cyclohexane.mol
CONFLEX 20090416043D 1 1.00000 -3.56094 1
D3D ,E = -3.561, G = 0.325E-08, P = 99.9955, M( 0), IFN =00000001-00000001
18 18 0 0 999 V2000
-1.2627 0.7290 0.2258 C 0 0 0 0 0
-0.0000 1.4580 -0.2258 C 0 0 0 0 0
-1.2627 -0.7290 -0.2258 C 0 0 0 0 0
-2.1462 1.2391 -0.1742 H 0 0 0 0 0
-1.3365 0.7716 1.3195 H 0 0 0 0 0
0.0000 2.4782 0.1742 H 0 0 0 0 0
-0.0000 1.5433 -1.3195 H 0 0 0 0 0
-0.0000 -1.4580 0.2258 C 0 0 0 0 0
-2.1462 -1.2391 0.1742 H 0 0 0 0 0
-1.3365 -0.7716 -1.3195 H 0 0 0 0 0
-0.0000 -2.4782 -0.1742 H 0 0 0 0 0
-0.0000 -1.5433 1.3195 H 0 0 0 0 0
1.2627 -0.7290 -0.2258 C 0 0 0 0 0
2.1462 -1.2391 0.1742 H 0 0 0 0 0
1.3365 -0.7716 -1.3195 H 0 0 0 0 0
1.2627 0.7290 0.2258 C 0 0 0 0 0
1.3365 0.7716 1.3195 H 0 0 0 0 0
2.1462 1.2391 -0.1742 H 0 0 0 0 0
2 1 1 0 0
3 1 1 0 0
1 4 1 0 0
1 5 1 0 0
2 6 1 0 0
2 7 1 0 0
2 16 1 0 0
3 8 1 0 0
3 9 1 0 0
3 10 1 0 0
11 8 1 0 0
12 8 1 0 0
13 8 1 0 0
14 13 1 0 0
13 15 1 0 0
16 13 1 0 0
16 17 1 0 0
16 18 1 0 0
M END
> <DATE_YYYY/MM/DD>
2020/09/04
> <TIME_HH:MM:SS.XX>
16:04:19.46
> <MOL_FILE_NAME>
Cyclohexane-F: Cyclohexane.mol
> <FORCE_FIELD_NAME>
MMFF94S(2010-12-04HG)
> <TEMPERATURE_K>
298.15
> <TOTAL_NUMBER_OF_CONFORMERS>
2
> <CONFORMER_ID>
00000001
> <POTENTIAL_ENERGY_KCAL/MOL>
-3.560936
> <ENERGY_RMS_GRADIENT_KCAL/MOL/ANGS>
3.2500000E-09
> <BOLTZMANN_POPULATION_%>
99.99550
> <TOTAL_GIBBS_FREE_ENERGY_KCAL/MOL>
84.57302
> <TOTAL_ENTHALPY_KCAL/MOL>
105.5726
> <TOTAL_ENTROPY_CAL/MOL/K>
70.43294
> <HEAT_CAPACITY_CAL/MOL/K>
24.41534
> <ENTHALPY_FUNCTION_CAL/MOL/K>
13.69442
> <FREE_ENERGY_FUNCTION_CAL/MOL/K>
56.73852
> <CHIRALITY>
F
> <SYMMETRY_NUMBER>
6
> <POINT_GROUP>
D3D
> <NUMBER_OF_NEGATIVE_EIGENVALUES>
0
> <CONFLEX_PERTURBATION_FLAG>
T
> <CONFLEX_REOPTIMIZATION_FLAG>
F
$$$$
[Expansion of conformation search space]
Refer to Cyclohexane-F.ls1 in the previous section, the second conformer shows “F” in “INIT.”. This means that the second conformer has not yet been used as initial structure in the search. It may be possible to derive other new conformers by employing the second conformer as initial structure.
Therefore, we restart the conformation search by using the fxf file and perform the expanded search in using the second conformer as initial structure.
[Execution by Interface]
Open Cyclohexane-F.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and select [Conformation Search] in the pull-down menu of [Calculation Type:] on the calculation setting dialog displayed.
Edit the value of [Search Limit:] to 6.0. This is because the energy difference between the most stable conformer and the second most stable conformer is 5.9297 kcal/mol. By this setting, the second most stable conformer will be used as initial structure in the search.
When the calculation settings are complete, click . The calculation will start.
After finishing this calculation, the search of area within 6.0 kcal/mol from the most stable conformer on conformational space is completed.
In the expanded search calculation, Cyclohexane-F.fxf file which was obtained by the previous search is needed in the folder containing Cyclohexane-F.mol and Cyclohexane-F.ini files.
[Execution by command line]
Edit the value of [SEL=] to 6.0 in Cyclohexane-F.ini file.
This is because the energy difference between the most stable conformer and the second most stable conformer is 5.9297 kcal/mol. By this setting, the second most stable conformer will be used as initial structure in the search.
Cyclohexane-F.ini file
MMFF94S CONFLEX SEARCH=ENERGY SEL=6.0
Store the three files of Cyclohexane-F.mol, Cyclohexane-F.ini, and Cyclohexane-F.fxf in an one folder, and execute below command. The calculation will start.
After finishing this calculation, the search of area within 6.0 kcal/mol from the most stable conformer on conformational space is completed.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par Cyclohexane-Fenter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
Calculation results
If you check Cyclohexane-F.ls1, you can see that the value of INIT. of the second conformer has changed to “T”, that is, this indicates that the second conformer was used as initial structure in the search.
====================================================================================
CONF. ORIGINAL DISTRI- NO.
NO. ID STERIC E DELTA E BUTION INIT. REOPT. NEG.
------------------------------------------------------------------------------------
1 00000001 -3.5609 0.0000 99.9955 T F 0
2 00000002 2.3688 5.9297 0.0045 T* F 0
------------------------------------------------------------------------------------
MINIMUM ENERGY: -3.5609 KCAL/MOL
AVERAGE ENERGY: -3.5607 KCAL/MOL (BASED ON THE BOLTZMANN LAW)
====================================================================================
As the results, we couldn't get any new conformers in the expanded search. Therefore, it can be considered that the search for all energy minimum structures searchable using CONFLEX algorithm and MMFF94s force field has been completed.
The region on the conformational space to be searched can be expanded by increasing the value of SEL according to information in the ls1 file and re-executing the search calculation. When all conformers found are used as initial structure and the search does not obtain new conformers, it can be considered to completely cover the conformational space generated by the force field used.
[Visualization of calculation results]
[If you executed the calculation by using Interface]
After submitting a job, Job Manager is appeared at bottom of CONFLEX Interface. Job Manager shows a state of the job.
Confirm the state of the search job is “Finished”, and double-click the row of the job (red frame part). Cyclohexane-F.sdf file will open, and visualize conformers found.
* The function of screen dividing can control by values of [Columns/Rows] of the tool bar displayed by selecting [Controller] in View menu.
[If you executed the calculation by using command line]
There is Cyclohexane-F.sdf file in the folder containing the input files. Open the Cyclohexane-F.sdf file. The conformers found will be visualized.
* The function of screen dividing can control by values of [Columns/Rows] of the tool bar displayed by selecting [Controller] in View menu.
[Conformation search with solvent effect]
This section explains a conformation search with solvent effect by using GB/SA model.
About explanation of GB/SA model, please refer to [Calculation with solvent effect].
We use a zwitterionic glycine dimer.
Structure data of the zwitterionic glycine dimer (gly2.mol)
gly2.mol
17 16 0 0 0 0 0 0 0 0999 V2000
-1.2219 0.9765 -2.1504 N 0 3 0 0 0 0 0 0 0 0 0 0
0.2781 0.9765 -2.1504 C 0 0 0 0 0 0 0 0 0 0 0 0
0.6496 2.0256 -2.1504 H 0 0 0 0 0 0 0 0 0 0 0 0
0.7803 0.2658 -0.9176 C 0 0 0 0 0 0 0 0 0 0 0 0
1.9679 0.1552 -0.7258 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.1098 -0.2537 -0.0165 N 0 0 0 0 0 0 0 0 0 0 0 0
0.3728 -0.9366 1.1681 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9911 -0.2372 1.7741 H 0 0 0 0 0 0 0 0 0 0 0 0
-0.8018 -1.4089 1.9892 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6088 -2.0256 3.0592 O 0 0 0 0 0 0 0 0 0 0 0 0
-1.9679 -1.1835 1.5993 O 0 5 0 0 0 0 0 0 0 0 0 0
-1.5708 0.4839 -3.0034 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5698 0.4832 -1.2973 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.5701 1.9618 -2.1504 H 0 0 0 0 0 0 0 0 0 0 0 0
0.6489 0.4518 -3.0592 H 0 0 0 0 0 0 0 0 0 0 0 0
-1.1047 -0.1611 -0.1772 H 0 0 0 0 0 0 0 0 0 0 0 0
0.9910 -1.8114 0.8658 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
1 12 1 0
1 13 1 0
1 14 1 0
2 3 1 0
2 4 1 0
2 15 1 0
4 5 2 0
4 6 1 0
6 7 1 0
6 16 1 0
7 8 1 0
7 9 1 0
7 17 1 0
9 10 2 0
9 11 1 0
M END
[Execution by Interface]
Open the gly2.mol file by CONFLEX Interface.
Select [CONFLEX] in Calculation menu, and click in the calculation setting dialog displayed.
Select [Conformation Search] in the pull-down menu of [Calculation Type:] in [General Settings] dialog on the detail setting dialog.
Next, select [GB/SA] in the pull-down menu of [Solvent Effect] in [Force Field] dialog on the detail setting dialog.
Finally, edit the value of [Search Limit:] to [10.0] in [Conformation Search] dialog. After finishing this calculation, the search of area within 10.0 kcal/mol from the most stable conformer on conformational space is completed.
When the calculation settings are complete, click . The calculation will start.
[Execution by command line]
The calculation settings are defined by describing keywords in the gly2.ini file.
gly2.ini file
MMFF94S GBSA CONFLEX SEL=10.0
| Keyword | Explanation |
|---|---|
| MMFF94S | Use MMFF94s force filed |
| GBSA | Introduce solvent effect by GB/SA model |
| CONFLEX | Execute a conformation search |
| SEL=10.0 | Search limit. Conformers found in the region within 10.0 kcal/mol from the most stable conformer are selected as initial structure. |
Store the gly2.mol and gly2.ini files in an one folder, and execute below command. The calculation will start.
C:\CONFLEX\bin\flex9a_win_x64.exe -par C:\CONFLEX\par gly2enter
The above command is for Windows OS. For the other OS, please refer to [How to execute CONFLEX].
Calculation results
The structure of the most stable conformer is shown below. About how to visualize that, please refer to [Visualization of calculation results].
