CN112233733A - Molecular force field quality control system and control method thereof - Google Patents
Molecular force field quality control system and control method thereof Download PDFInfo
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Abstract
The invention provides a molecular force field quality control system and a control method thereof, wherein the molecular force field quality control system comprises a data acquisition module, a data acquisition module and a data processing module, wherein the data acquisition module is used for reading quantum mechanical optimization data of a target and molecular mechanical optimization data of a force field to be detected and arranging the data into a data table and a molecular coordinate file containing specified columns; the energy analysis module is used for calculating evaluation indexes related to the molecular conformation energy and the potential energy surface of the index set; calculating an energy analysis index according to two test method parameters to generate an original data table; the structure analysis module is used for calculating evaluation indexes related to the molecular structures of the index set; calculating a structural analysis index to generate an original data table; and the data statistics module is used for calculating statistical indexes, printing statistical data and drawing a statistical chart. The invention brings the force field parameter items into the quality control flow, and the force field developer can accurately identify the parameter items with poor performance in the test set and carry out parameter optimization in a targeted manner.
Description
Technical Field
The invention belongs to the field of molecular mechanics, and particularly relates to a molecular force field quality control system and a control method thereof, which are used as a method for testing intramolecular parameter performance in a force field and are suitable for evaluating parameters in the molecular force field and fitting and correcting parameters with poor performance.
Background
Molecular mechanics has wide applications in various fields such as drug design, material science and the like due to lower calculation cost and higher calculation precision. Molecular mechanics uses specific functions to calculate molecular properties (such as structure and energy), and the form of the function and the parameters in the function are called molecular force field. The energy of a commonly used force field can be decomposed into two major parts, a bonding (intramolecular) part and a non-bonding (intermolecular) part, wherein the bonding part describes the vibration and rotation of a chemical bond in a molecule and comprises bond length, bond angle, dihedral angle and out-of-plane bending parameters, and the non-bonding part describes the attraction or repulsion of atoms in a molecule or a molecule which are far away and caused by static electricity and van der waals force, and comprises a charge model and van der waals parameters.
Because the model of the molecular force field itself contains approximate processing, and the parameters are derived from quantum chemical computation result fitting or empirical rules of a large number of molecules, the coverage of the training set affects the application range of the parameters, and the similarity inside the training set affects the accuracy of the parameters, the generality and the accuracy of the force field need to be balanced, which causes the difference of the accuracy of most force fields on target molecules. In force field development and application, it is necessary to evaluate and validate a particular test set to obtain quality control data.
In the current literature reports of open source or commercial force fields, the used evaluation indexes are not uniform, the index definition is not clear, the difference of a test set is large, the calculation process is usually coupled with the data analysis process, a large amount of data is not disclosed, and a perfect evaluation method and an index system are lacked. Researchers and commercial users generally have no condition to carry out quantitative method verification on the selected force field under a special use scene, and data support is obtained. A set of complete and independent quality control flow is beneficial to selecting and optimizing force field parameters under different scenes, and a more accurate molecular mechanics calculation result is obtained.
Disclosure of Invention
Aiming at the technical problems, the invention provides a molecular force field quality control system and a control method thereof, which take molecular conformation energy and structure optimized by a high-precision quantum chemistry method as a standard, and test and evaluate the energy and structure deviation between the molecular mechanics calculation results of different force fields and the standard.
The specific technical scheme is as follows:
the molecular force field quality control system comprises a data acquisition module, an energy analysis module, a structure analysis module and a data statistics module;
the data acquisition module selects a corresponding calculation simulation tool to generate quantum mechanical optimization data for a target and molecular mechanical optimization data for a force field to be tested according to the molecular source of the test set, the source of the force field to be tested and user preference, and arranges the data into a data table and a molecular coordinate file containing specified columns to serve as input data of the energy analysis module;
the energy analysis module is used for calculating evaluation indexes related to the molecular conformation energy and the potential energy surface of the index set; a program reads a molecular name, a dihedral angle atomic number, an angle and conformation energy which are provided by a user and are limited and optimized, calculates an energy analysis index according to two test method parameters, and generates an original data table;
the structure analysis module is used for calculating evaluation indexes related to the molecular structures of the index set; reading the molecular name, the dihedral angle atomic number for limiting optimization and the 3D coordinate provided by a user by a program, calculating a structural analysis index, and generating an original data table;
the data statistics module comprises a series of general statistics and mapping programs for energy analysis and structural analysis, can read an original data table of energy and structural analysis results, call a corresponding program, calculate statistical indexes, print statistical data and draw a statistical chart.
The data acquisition module selects corresponding tools according to specific conditions, other modules are all realized by Python programs, and the Python programs relate to numpy, scipy, pandas, matplotlib and rdkit libraries and integrate index calculation, data statistics and drawing processes into Jupyter notebooks.
The control method of the molecular force field quality control system comprises the following steps:
(1) preparation of high-precision QM data, which is quantum chemistry data: selecting a target test set, using quantum chemical calculation software, and performing potential energy surface scanning on the rotatable dihedral angle of the molecule by using a high-precision quantum chemical method, wherein the scanning interval is generally 15 or 30 degrees, and the obtained energy EQMAnd the coordinate rQMIs used for benchmarking;
(2) preparing molecular mechanics data (namely MM data) of a force field to be measured: taking the conformation in the step (1) as an input conformation, respectively using one or more force fields to be tested to carry out molecular mechanics optimization for more than 1000 steps, and obtaining energy data EMM1，EMM2… is stored in tabular format with energy units of kcal/mol and structural data stored in.mol or.sdf format;
(3) energy translation: inputting data tables, E for each rotatable dihedral angleQMAnd EMMiPerforming a translation, i being 1,2, …, such that the energy minimum point of E is 0; eMMiThere are two alternative translation strategies, 0 and min and E for the lowest point, respectivelyQMThe variance of (a);
(4) the energy analysis module calculates single conformation energy related indexes and potential energy surface related indexes in sequence, and specific potential energy surface drawing can be extracted for checking;
(5) the structure analysis module calculates RMSD and key length, key angle and dihedral angle related indexes in sequence, and force field developers can additionally input parameter item data tables and calculate parameter item related indexes;
(6) and (5) reading the calculation results in the step (4) and the step (5) by the data statistics module, defining the colors and labels of the pictures and the tables, and outputting statistical data and a report.
The molecular force field quality control system and the control method thereof provided by the invention have the following technical advantages:
(1) the standardized index set for controlling the molecular force field quality is specified.
(2) A series of indexes which are not reported in the literature and are used for evaluating the similarity between the dihedral potential energy surface shape and the QM potential energy surface are provided.
(3) The force field parameter items are brought into the quality control process, and a force field developer can accurately identify the parameter items with poor performance in the test set, so that parameter optimization is performed in a targeted manner.
(4) The index calculation and data analysis tool is decoupled from commercial software, and can process and analyze calculation data with wide sources.
(5) Index calculation, data statistics and drawing processes are integrated into the Jupiter notebook to realize visualization.
Drawings
FIG. 1 is a flow chart of the molecular force field quality control according to the present invention;
FIG. 2 is a potential energy surface diagram of an embodiment;
FIG. 3 is a molecular structure diagram of an embodiment;
FIG. 4a is the example QM conformational energy correlation;
FIG. 4b is the energy dependence of the MM conformation of the example;
FIG. 5a is the QM energy dependence of the potential surface minima of an embodiment;
FIG. 5b is MM energy dependence of the potential energy surface minima of an embodiment;
FIG. 6 is a potential energy surface RMSE distribution of an embodiment;
FIG. 7 is a distribution of the potential surface minima correlation coefficient R for an embodiment;
FIG. 8 is a distribution of the potential energy surface correlation coefficient R of an embodiment;
FIG. 9 is a diagram of an embodiment of a deviation of a small position (angle) of an extreme value of a potential energy surface;
FIG. 10a is a two-dimensional distribution of potential energy surface minima energies and position errors for an example GAFF2 force field;
FIG. 10b is a two-dimensional distribution of potential energy surface minima energies and position errors for an embodiment OpenFF force field;
FIG. 11 is a Root Mean Square Displacement (RMSD) distribution of an embodiment;
FIG. 12 is a key length deviation distribution of an embodiment;
FIG. 13 is a key angle deviation distribution of an embodiment;
FIG. 14 is a non-fixed dihedral angle deviation distribution of an embodiment.
Detailed Description
The specific technical scheme of the invention is described by combining the embodiment.
The specific technical scheme is as follows:
the molecular force field quality control indexes are shown in Table 1. The index set defines a series of indexes that evaluate the performance of the force field parameters on the test set.
TABLE 1 set of molecular force field quality control indexes
The molecular force field quality control system comprises a data acquisition module, an energy analysis module, a structure analysis module and a data statistics module;
the data acquisition module can select corresponding tools according to specific conditions, other modules are all realized by Python programs, and relate to numpy, scipy, pandas, matplotlib and rdkit libraries, and index calculation, data statistics and drawing processes are integrated into Jupyter notebook. The flow architecture can remove the dependence on business software, is convenient for users and developers with scientific computing backgrounds to use, and simultaneously realizes visualization.
The data acquisition module can select a corresponding calculation simulation tool to generate quantum mechanical optimization data for the target and molecular mechanical optimization data for the force field to be tested according to the test set molecular source, the force field source to be tested and the user preference, and the data acquisition module is arranged into a data table and a molecular coordinate file containing designated columns and used as input data of the analysis module.
And the energy analysis module calculates evaluation indexes related to the molecular conformation energy and the potential energy surface of the index set. And reading the molecular name, the dihedral angle atomic number for limiting optimization, the angle and the conformational energy provided by a user by a program, calculating an energy analysis index according to two test method parameters, and generating an original data table.
And the structure analysis module calculates evaluation indexes related to the molecular structures of the index set. And reading the molecular name, the dihedral angle atomic number for limiting optimization and the 3D coordinate provided by the user by the program, calculating a structural analysis index, and generating an original data table.
The data statistics module comprises a series of general statistics and mapping programs for energy analysis and structural analysis, and can read an original data table of energy and structural analysis results, call a corresponding program, calculate statistical indexes, print statistical data and draw a statistical chart.
As shown in fig. 1, the control method of the molecular force field quality control system comprises the following steps:
(1) high precision quantum chemistry data (QM data) preparation: selecting target test set, and performing potential energy surface scan on rotatable dihedral angle of the molecule by high-precision quantum chemistry method (such as B3LYP/6-31G (d)) with quantum chemical calculation software (such as PSI4), wherein the scan interval is 15 or 30 degrees, and the obtained energy EQMAnd the coordinate rQMFor benchmarking.
(2) Preparing molecular mechanics data (MM data) of the force field to be measured: taking the conformation in the step (1) as an input conformation, respectively using one or more force fields to be tested to carry out molecular mechanics optimization for more than 1000 steps, and obtaining energy data EMM1，EMM2… is stored in the format shown in Table 2, with energy units in kcal/mol, and structural data in the.mol or.sdf format.
Table 2 input data table
(3) Energy translation: enter the Table shown in Table 2, E for each rotatable dihedral angleQMAnd EMMi(i-1, 2, …) so that the energy minimum point of E is 0. EMMiThere are two alternative translation strategies, 0 and min and E for the lowest point, respectivelyQMThe variance of (c).
(4) The energy analysis module calculates the single conformation energy related index and the potential energy surface related index in turn, and specific potential energy surface drawing can be extracted for checking.
(5) The structure analysis module calculates RMSD and key length, key angle and dihedral angle related indexes in sequence, and force field developers can additionally input parameter item data tables to calculate parameter item related indexes.
(6) And (4) reading the calculation results of the step (4) and the step (5), defining the colors and labels of the pictures and the tables, and outputting statistical data and reports, such as tables 3-5 and fig. 4 a-14.
This example takes the Roche test set as an example, where the test set contains 459 molecules with a rotatable dihedral angle, and evaluates the performance of two open source force fields GAFF2 and OpenFF. Downloading QM potential energy surface scanning energy and structure from a publicly released webpage, obtaining MM data of a GAFF2 force field by Amber software, calculating the MM data of the OpenFF force field by OpenMM software, making an energy table as shown in Table 2, and storing molecular coordinates in a.mol format.
And analyzing the energy table by using an energy analysis module to obtain a QC energy analysis data table which comprises QC index values of single conformations.
And analyzing the molecular coordinates by using a structure analysis module to obtain RMSD, a bond length, a bond angle and a dihedral angle data table.
The data statistics module is used to generate statistics and reports as shown in tables 3-5, fig. 4 a-14.
TABLE 3 test parameters, conformational energy bias, dihedral angle RMSE and correlation coefficient R statistics
TABLE 4 matching rate of extreme points of potential energy surface
Table 5 structural index print results example
As can be seen from the statistical report, OpenFF generally has a smaller deviation than GAFF2 in most of the energy indexes shown in table 3 and fig. 4a to 8, and the performance is better; however, in terms of description of the potential energy surface shape, the potential energy surface correlation coefficients R and GAFF2 in table 3 perform equivalently to OpenFF, and the potential energy surface minimum and global minimum matching rate shown in table 4 and the error two-dimensional distribution of minimum energy and position shown in fig. 10a and 10b perform slightly better than even OpenFF in terms of accurate matching of the potential energy surface shape in GAFF 2. In terms of structure, the statistical indicators in table 5 and the indicator distributions in fig. 11-14 show that OpenFF still performs slightly better than GAFF2 in both RMSD and dihedral angle deviation, which are more important for the quality of the force field.
After the potential surface correlation coefficients are sorted, the correlation coefficient R of the GAFF2 potential surface of 006-C12H12N2 molecules and the QM result is found to be less than 0, a negative correlation is shown, and the GAFF2 force field does not perform well. By extracting the potential energy surface data to plot a potential energy surface map as shown in FIG. 2 and the molecular structure as shown in FIG. 3, the molecules in which the dihedral angles are located can be located to belong to the class of secondary aromatic amines, in this case angles C3-N4-C11-C10. The potential energy surface energy barrier is less than 5kcal/mol, the energy barrier for dihedral rotation is low, but the description of the GAFF2 force field for extreme point positions is wrong. Therefore, when the user needs to calculate the molecules of the secondary aromatic amines, other force fields can be selected, and the force field developer can consider optimizing the parameters of the molecules.
Claims (3)
1. The molecular force field quality control system is characterized by comprising a data acquisition module, an energy analysis module, a structure analysis module and a data statistics module;
the data acquisition module selects a corresponding calculation simulation tool to generate quantum mechanical optimization data for a target and molecular mechanical optimization data for a force field to be tested according to the molecular source of the test set, the source of the force field to be tested and user preference, and arranges the data into a data table and a molecular coordinate file containing specified columns to serve as input data of the energy analysis module;
the energy analysis module is used for calculating evaluation indexes related to the molecular conformation energy and the potential energy surface of the index set; a program reads a molecular name, a dihedral angle atomic number, an angle and conformation energy which are provided by a user and are limited and optimized, calculates an energy analysis index according to two test method parameters, and generates an original data table;
the structure analysis module is used for calculating evaluation indexes related to the molecular structures of the index set; reading the molecular name, the dihedral angle atomic number for limiting optimization and the 3D coordinate provided by a user by a program, calculating a structural analysis index, and generating an original data table;
the data statistics module comprises a series of general statistics and mapping programs for energy analysis and structural analysis, can read an original data table of energy and structural analysis results, call a corresponding program, calculate statistical indexes, print statistical data and draw a statistical chart.
2. The molecular force field quality control system of claim 1, wherein the data acquisition module selects corresponding tools according to specific situations, and the other modules are implemented by Python programs, which relate to numpy, scipy, pandas, matplotlib and rdkit libraries, and integrate index calculation, data statistics and drawing processes into Jupyter notebook.
3. The control method of the molecular force field quality control system according to claim 1 or 2, characterized by comprising the steps of:
(1) preparation of high-precision QM data, which is quantum chemistry data: selecting a target test set, using quantum chemical calculation software, and performing potential energy surface scanning on the rotatable dihedral angle of the molecule by using a high-precision quantum chemical method, wherein the scanning interval is generally 15 or 30 degrees, and the obtained energy EQMAnd the coordinate rQMIs used for benchmarking;
(2) preparing molecular mechanics data (namely MM data) of a force field to be measured: to be provided withTaking the conformation in the step (1) as an input conformation, respectively carrying out molecular mechanics optimization for more than 1000 steps by using one or more force fields to be tested, and obtaining energy data EMM1，EMM2… is stored in tabular format with energy units of kcal/mol and structural data stored in.mol or.sdf format;
(3) energy translation: inputting data tables, E for each rotatable dihedral angleQMAnd EMMiA translation is performed, i =1,2, …, making the value of the energy minimum point of E0; eMMiThere are two alternative translation strategies, 0 and min and E for the lowest point, respectivelyQMThe variance of (a);
(4) the energy analysis module calculates single conformation energy related indexes and potential energy surface related indexes in sequence, and specific potential energy surface drawing can be extracted for checking;
(5) the structure analysis module calculates RMSD and key length, key angle and dihedral angle related indexes in sequence, and force field developers can additionally input parameter item data tables and calculate parameter item related indexes;
(6) and (5) reading the calculation results in the step (4) and the step (5) by the data statistics module, defining the colors and labels of the pictures and the tables, and outputting statistical data and a report.
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