CN112199909A - Method for accurately calculating absolute free energy of gas molecules - Google Patents
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- 238000000034 method Methods 0.000 title claims abstract description 20
- 238000005182 potential energy surface Methods 0.000 claims abstract description 21
- 230000004888 barrier function Effects 0.000 claims abstract description 12
- 238000005381 potential energy Methods 0.000 claims abstract description 10
- 230000008859 change Effects 0.000 claims abstract description 7
- 238000004088 simulation Methods 0.000 claims description 17
- 241000860832 Yoda Species 0.000 claims description 3
- 238000009795 derivation Methods 0.000 claims description 3
- 230000008863 intramolecular interaction Effects 0.000 claims 1
- 238000004364 calculation method Methods 0.000 abstract description 12
- 230000008569 process Effects 0.000 abstract description 3
- 239000007788 liquid Substances 0.000 description 7
- 239000001273 butane Substances 0.000 description 4
- IJDNQMDRQITEOD-UHFFFAOYSA-N n-butane Chemical compound CCCC IJDNQMDRQITEOD-UHFFFAOYSA-N 0.000 description 4
- OFBQJSOFQDEBGM-UHFFFAOYSA-N n-pentane Natural products CCCCC OFBQJSOFQDEBGM-UHFFFAOYSA-N 0.000 description 4
- 238000000329 molecular dynamics simulation Methods 0.000 description 3
- 239000013078 crystal Substances 0.000 description 2
- 230000003993 interaction Effects 0.000 description 2
- 238000005070 sampling Methods 0.000 description 2
- 239000007787 solid Substances 0.000 description 2
- 230000004075 alteration Effects 0.000 description 1
- 230000009286 beneficial effect Effects 0.000 description 1
- SYRIRLOOSKFSFC-UHFFFAOYSA-N butane Chemical compound CCCC.CCCC SYRIRLOOSKFSFC-UHFFFAOYSA-N 0.000 description 1
- 238000009792 diffusion process Methods 0.000 description 1
- 239000003814 drug Substances 0.000 description 1
- 229940079593 drug Drugs 0.000 description 1
- 230000010354 integration Effects 0.000 description 1
- 238000002844 melting Methods 0.000 description 1
- 230000008018 melting Effects 0.000 description 1
- 238000012986 modification Methods 0.000 description 1
- 230000004048 modification Effects 0.000 description 1
- 238000012900 molecular simulation Methods 0.000 description 1
- 238000012216 screening Methods 0.000 description 1
- 238000007614 solvation Methods 0.000 description 1
- 238000000859 sublimation Methods 0.000 description 1
- 230000008022 sublimation Effects 0.000 description 1
- 238000006467 substitution reaction Methods 0.000 description 1
- 238000012795 verification Methods 0.000 description 1
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Abstract
The invention discloses a method for accurately calculating absolute free energy of gas molecules, which comprises the following steps: s1, reducing the energy barrier of the flexible dihedral angle potential energy surface in the gas molecules; and S2, calculating absolute free energy of gas molecules. The invention realizes the automatic identification and potential energy surface scanning of flexible dihedral angles in molecules, realizes the fitting of the dihedral angle potential energy surface, automatically modifies the dihedral angle parameters to reduce the potential energy surface to a specific value, realizes a new WHAM program, can obtain actual free energy from potential energy reweights of biased and unbiased, designs a set of feasible calculation flow, and realizes the gradual change of potential energy when gas molecules gradually remove various types of energy; all the processes are connected together, and the automatic calculation of the absolute free energy of the gas molecules is realized.
Description
Technical Field
The invention belongs to the technical field of molecular dynamics simulation, and particularly relates to a method for accurately calculating absolute free energy of gas molecules.
Background
In recent years, molecular simulation techniques have been widely used, and there has been an increasing demand for free energy calculations. Currently, because the stability of a crystal structure is better and the sampling space is relatively smaller, some methods can accurately predict the absolute free energy of a solid molecule and can be applied to prediction and screening of a stable experimental crystal form of a drug molecule.
There is no good accurate prediction method for the absolute free energy of liquid and gas molecules. This makes it impossible to predict the properties related to solid-liquid (e.g. melting point, solubility), solid-gas (e.g. enthalpy of sublimation), etc. very effectively.
The calculation of the absolute free energy of gas molecules and liquid molecules currently has no very effective method:
for gas molecules, due to the extremely complex potential energy surface, the gas molecules are easy to fall into the local energy lowest point during simulation, thereby influencing the convergence of the free energy calculation result.
For liquid molecules, the situation is more complicated, and not only the influence of the potential energy surface of the liquid molecules is needed to be overcome, but also the sampling problem caused by the rapid diffusion of the molecules is also overcome. Therefore, it is more difficult to accurately calculate the absolute free energy of the liquid molecules.
Disclosure of Invention
In view of the above technical problems, the present invention provides a method for accurately calculating the absolute free energy of gas molecules, which can accurately calculate the absolute free energy of solid and gas, and can indirectly calculate the absolute free energy of liquid molecules by calculating the solvation free energy.
In order to achieve the purpose, the invention provides the following technical scheme:
a method for accurately calculating the absolute free energy of a gas molecule, comprising the steps of:
s1, reducing the energy barrier of the flexible dihedral angle potential energy surface in the gas molecules;
s1.1, preparing a coordinate file of a molecule to be calculated, and grabbing force field parameters through a related tool;
s1.2, calling yoda program, loading molecular coordinates and a force field, and searching all flexible dihedral angles in molecules;
s1.3, potential energy surface scanning is carried out on all the found flexible dihedral angles;
s1.4, fitting a dihedral angle potential energy surface with an energy barrier larger than 5kcal/mol in the potential energy surface, modifying corresponding dihedral angle parameters, and reducing the energy barrier;
s1.5 repeating steps S1.3 and S1.4 until no energy barrier greater than 5kcal/mol exists in the potential energy planes of all compliant angles;
s1.6, generating a new force field parameter file;
s2, calculating absolute free energy of gas molecules;
s2.1, establishing a simulation box with the size of 20nm multiplied by 20nm by using new force field parameters, carrying out NVT simulation at a series of temperatures, and calculating the electrostatic acting force by using a cut-off mode, wherein the step length is 1fs, and the simulation is 10 ns;
s2.2, selecting two balance structures at reference temperature as initial structures of free energy simulation;
s2.3 stepwise limiting the position of a central heavy atom, the force constant varying from 0 to 10000kJ/mol/nm2The step is difficult to converge by calculating the free energy through MD simulation, but can be derived from theory;
s2.4 stepwise limiting the position of other heavy atoms, the force constant varying from 0 to 10000kJ/mol/nm2；
S2.5 stepwise limiting the position of the non-heavy atoms, the force constant varying from 0 to 10000kJ/mol/nm2；
S2.6 stepwise increasing the position restriction of all atoms, the force constant varying from 10000 to 200000kJ/mol/nm2；
S2.7 step-by-step removal of all atomic intramolecular (electrostatic, van der waals, bond, angle, dihedral) interactions;
s2.8, after the simulation is normal, all using the original force field parameters to rerun the track to obtain the unbound potential energy;
s2.9, loading the binary and unbiased energy of each lambda or T window by using the modified WHAM program to obtain the final free energy after reweigh;
s2.10 uses the reweight Δ f (T) and PSCP free energy and related theoretical derivation values to calculate the final absolute free energy change with temperature.
Wherein, the related tool in step S1.1 is antechamber or CHARMM-GUI.
The series of temperatures in the step S2.1 are within the range of 100-400K.
Step S2.2 selects two reference temperatures of 200K and 300K.
Compared with the prior art, the invention has the beneficial effects that:
(1) and the automatic identification of flexible dihedral angles in molecules and the potential energy surface scanning are realized.
(2) Fitting the dihedral angle potential energy surface is realized, and the dihedral angle parameters are automatically modified so as to reduce the potential energy surface to a specific value.
(3) A new WHAM program is realized, and the actual free energy can be obtained from the potential energies reweigh of biased and unbound.
(4) A set of feasible calculation process is designed to realize the gradual change of potential energy when the gas molecules gradually remove various energies.
(5) All the processes are connected together, and the automatic calculation of the absolute free energy of the gas molecules is realized.
Drawings
FIG. 1 is a schematic representation of the molecular structure of butane in accordance with the examples;
FIG. 2 is a dihedral angle potential profile of an example butane molecule initial C _ C1_ C2_ C3;
FIG. 3 is a potential energy surface obtained by scanning according to an embodiment;
FIG. 4 is a flow chart of the calculation of absolute free energy of gas molecules according to the present invention;
FIG. 5 is an absolute free energy curve obtained using an original force field;
FIG. 6 is a plot of the absolute free energy obtained by the WHAM program reweight using the new force field in this example.
Detailed Description
The technical solutions in the embodiments of the present invention will be clearly and completely described below with reference to the drawings in the embodiments of the present invention, and it is obvious that the described embodiments are only a part of the embodiments of the present invention, and not all of the embodiments. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present invention.
This example uses the calculation procedure of the absolute free energy of butane (butane) molecule, as shown in FIG. 1:
(1) preparing a coordinate (pdb) file of butane molecules, and grabbing corresponding GAFF2 force field parameters by using antechamber;
(2) calling yoda program, loading molecular coordinates and force field, and searching all flexible dihedral angles in molecules;
(3) potential energy surface scanning is carried out on all the found flexible dihedral angles;
the butane molecule has only one flexible dihedral angle (C _ C1_ C2_ C3) as shown in fig. 2.
(4) Fitting a dihedral angle potential surface with an energy barrier larger than 5kcal/mol in the potential surface, modifying corresponding dihedral angle parameters, and reducing the energy barrier;
fitting function:
f(x)＝k1*(1+cosx)+k2*(1-cos2x)+k3*(1+cos3x)+k4*(1+cos4x)+k6*(1+cos6x)+b
(5) repeating steps (3) and (4) until no energy barrier greater than 5kcal/mol exists in the potential energy surfaces of all the flexible angles; after modifying the dihedral angle parameter C _ C1_ C2_ C3, scanning the obtained potential energy surface, as shown in FIG. 3;
(6) generating a new force field parameter file;
the flow of calculation of the absolute free energy of the gas molecules is shown in FIG. 4.
(7) Establishing a 20nm multiplied by 20nm simulated box by using new force field parameters, carrying out NVT simulation under a series of temperatures (100-400K), and calculating the electrostatic acting force by using a cut-off mode, wherein the step size is 1fs and the simulation is 10 ns;
through the potential energy data H (T) obtained by simulation at a series of temperatures, the non-dimensional change of the free energy along with the temperature Δ f (T) can be obtained by integration:
(8) selecting a balance structure under two reference temperatures (200K and 300K for convergence verification) as an initial structure of free energy simulation;
(9) gradually limiting the position of a central heavy atom, and changing the force constant from 0 to 10000kJ/mol/nm2The step is difficult to converge by calculating the free energy through MD simulation, but can be derived from theory (Δ A)1)；
(10) The positions of other heavy atoms are gradually limited, and the force constant is changed from 0 to 10000kJ/mol/nm2(ΔA2)；
(11) The position of non-heavy atoms is gradually limited, and the force constant is changed from 0 to 10000kJ/mol/nm2(ΔA3)；
(12) The position limits of all atoms are gradually increased, and the force constant is changed from 10000 to 200000kJ/mol/nm2(ΔA4)；
(13) Intramolecular (electrostatic, van der waals, bond, angle, dihedral) interactions (Δ a) that gradually remove all atoms5)；
(14) After the simulation is normal, all the original force field parameters are used for rerun on the track to obtain the unbound potential energy;
the total PSCP free energy change (. DELTA.G) can be calculated by the above simulationPSCP(T))
(15) Loading the binary and unbiased energy of each lambda or T window by using the modified WHAM program to obtain the final free energy after reweigh;
the principle of the WHAM program for reweight:
calculation formula of standard WHAM:
(16) the change of the final absolute free energy with the temperature is calculated by using the delta f (T) and PSCP free energy after reweight and related theoretical derivation values.
The final absolute free energy is calculated as follows:
the results are shown in FIGS. 5 and 6.
From the calculation results, it can be seen that: the result of the new force field is combined with the free energy after reweight, and the convergence is obviously improved. This increase is more pronounced on more complex molecules.
Although embodiments of the present invention have been shown and described, it will be appreciated by those skilled in the art that changes, modifications, substitutions and alterations can be made in these embodiments without departing from the principles and spirit of the invention, the scope of which is defined in the appended claims and their equivalents.
Claims (6)
1. A method for accurately calculating the absolute free energy of a gas molecule is characterized by comprising the following steps:
s1, reducing the energy barrier of the flexible dihedral angle potential energy surface in the gas molecules;
and S2, calculating absolute free energy of gas molecules.
2. The method for accurately calculating the absolute free energy of gas molecules as claimed in claim 1, wherein the step S1 comprises the following sub-steps:
s1.1, preparing a coordinate file of a molecule to be calculated, and grabbing force field parameters through a related tool;
s1.2, calling yoda program, loading molecular coordinates and a force field, and searching all flexible dihedral angles in molecules;
s1.3, potential energy surface scanning is carried out on all the found flexible dihedral angles;
s1.4, fitting a dihedral angle potential energy surface with an energy barrier larger than 5kcal/mol in the potential energy surface, modifying corresponding dihedral angle parameters, and reducing the energy barrier;
s1.5 repeating steps S1.3 and S1.4 until no energy barrier greater than 5kcal/mol exists in the potential energy planes of all compliant angles;
s1.6, generating a new force field parameter file.
3. A method for accurately calculating the absolute free energy of a gas molecule according to claim 2, wherein the relevant tool in step S1.1 is antechamber or CHARMM-GUI.
4. The method for accurately calculating the absolute free energy of gas molecules as claimed in claim 1, wherein the step S2 comprises the following sub-steps:
s2.1, establishing a simulation box with the size of 20nm multiplied by 20nm by using new force field parameters, carrying out NVT simulation at a series of temperatures, and calculating the electrostatic acting force by using a cut-off mode, wherein the step length is 1fs, and the simulation is 10 ns;
s2.2, selecting two balance structures at reference temperature as initial structures of free energy simulation;
s2.3 stepwise limiting the position of a central heavy atom, the force constant varying from 0 to 10000kJ/mol/nm2Derived from theory;
s2.4 stepwise limiting the position of other heavy atoms, the force constant varying from 0 to 10000kJ/mol/nm2；
S2.5 stepwise limiting the position of the non-heavy atoms, the force constant varying from 0 to 10000kJ/mol/nm2；
S2.6 stepwise increasing the position restriction of all atoms, the force constant varying from 10000 to 200000kJ/mol/nm2；
S2.7 removing the intramolecular interactions of all atoms step by step;
s2.8, after the simulation is normal, all the original force field parameters are used for rerun on the track to obtain the unbound potential energy;
s2.9, loading the binary and unbiased energy of each lambda or T window by using the modified WHAM program to obtain the final free energy after reweigh;
s2.10 uses the reweigh Δ f (T) and PSCP free energies, and theoretical derivation values, to calculate the final absolute free energy change with temperature.
5. The method of claim 4, wherein the series of temperatures in step S2.1 is in the range of 100-400K.
6. The method according to claim 4, wherein the two reference temperatures of 200K and 300K are selected in step S2.2.
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| WO2023102870A1 (en) * | 2021-12-10 | 2023-06-15 | 上海智药科技有限公司 | Method and apparatus for computing free energy of molecule, and stability analysis method and apparatus, and device and storage medium |
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