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分子力场根据量子力学的波恩-奥本海默近似,一个分子的能量可以近似看作构成分子的各个原子的空间坐标的函数,简单地讲就是分子的能量随分子构型的变化而变化,而描述这种分子能量和分子结构之间关系的就是分子力场函数。分子力场函数为来自实验结果的经验公式,可以讲对分子能量的模拟比较粗糙,但是相比于精确的量子力学从头计算方法,分子力场方法的计算量要小数十倍,而且在适当的范围内,分子力场方法的计算精度与量子化学计算相差无几,因此对大分子复杂体系而言,分子力场方法是一套行之有效的方法。以分子力场为基础的分子力学计算方法在分子动力学、蒙特卡罗方法、分子对接等分子模拟方法中有着广泛的应用。
一般而言,分子力场函数由以下几个部分构成:
构成一套力场函数体系需要有一套联系分子能量和构型的函数,还需要给出各种不同原子在不同成键状况下的物理参数,比如正常的键长、键角、二面角等,这些力场参数多来自实验或者量子化学计算。
不同的分子力场会选取不同的函数形式来描述上述能量与体系构型之间的关系。到目前,不同的科研团队设计了很多适用于不同体系的力场函数,根据他们选择的函数和力场参数,可以分为以下几类
编辑 | 分子力场 | |
Developer(s) | Martin Karplus, Accelrys |
---|---|
Initial release | 1983 |
Stable release | c35b3 / 2009-08-15 |
Preview release | c36a3 / 2009-08-15 |
Written in | FORTRAN 77/95 |
Operating system | Unix-like |
Type | molecular dynamics |
License | The CHARMM Development Project |
Website | charmm.org |
CHARMM (Chemistry at HARvard Macromolecular Mechanics) is the name of a widely used set of force fields for molecular dynamics as well as the name for the molecular dynamics simulation and analysis package associated with them.[1][2] The CHARMM Development Project involves a network of developers throughout the world working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia.
The commercial version of CHARMM, called CHARMm (note the lowercase 'm'), is available from Accelrys.
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The CHARMM force fields for proteins include: united-atom (sometimes called "extended atom") CHARMM19[3], all-atom CHARMM22[4] and its dihedral potential corrected variant CHARMM22/CMAP.[5] In the CHARMM22 protein force field, the atomic partial charges were derived from quantum chemical calculations of the interactions between model compounds and water. Furthermore, CHARMM22 is parametrized for the TIP3P explicit water model. Nevertheless, it is frequently used with implicit solvents. In 2006, a special version of CHARMM22/CMAP was reparametrized for consistent use with implicit solvent GBSW.[6]
For DNA, RNA, and lipids, CHARMM27[7] is used. Some force fields may be combined, for example CHARMM22 and CHARMM27 for the simulation of protein-DNA binding. Additionally, parameters for NAD+, sugars, fluorinated compounds, etc. may be downloaded. These force field version numbers refer to the CHARMM version where they first appeared, but may of course be used with subsequent versions of the CHARMM executable program. Likewise, these force fields may be used within other molecular dynamics programs that support them.
In 2009, a general force field for drug-like molecules (CGenFF) was introduced. It "covers a wide range of chemical groups present in biomolecules and drug-like molecules, including a large number of heterocyclic scaffolds." [8] The general force field is designed to cover any combination of chemical groups. This inevitably comes with a decrease in accuracy for representing any particular subclass of molecules. Users are repeatedly warned in Mackerell's website not to use the CGenFF parameters for molecules for which specialized force fields already exist (as mentioned above for proteins, nucleic acids, etc).
CHARMM also includes polarizable force fields using two approaches. One is based on the fluctuating charge (FQ) model, also known as Charge Equilibration (CHEQ). [9][10] The other is based on the Drude shell or dispersion oscillator model. [11][12]
Parameters for all of these force fields may be downloaded from the Mackerell website for free.
The CHARMM program allows generation and analysis of a wide range of molecular simulations. The most basic kinds of simulation are minimization of a given structure and production runs of a molecular dynamics trajectory.
More advanced features include free energy perturbation (FEP), quasi-harmonic entropy estimation, correlation analysis and combined quantum, and molecular mechanics (QM/MM) methods.
CHARMM is one of the oldest programs for molecular dynamics. It has accumulated a huge number of features, some of which are duplicated under several keywords with slight variations. This is an inevitable result of the large number of outlooks and groups working on CHARMM throughout the world. The changelog file as well as CHARMM's source code are good places to look for the names and affiliations of the main developers. The involvement and coordination by Charles L. Brooks III's group at the University of Michigan is very salient.
Around 1969, there was considerable interest in developing potential energy functions for small molecules. CHARMM originated at Martin Karplus's group at Harvard. Karplus and his then graduate student Bruce Gelin decided the time was ripe to develop a program that would make it possible to take a given amino acid sequence and a set of coordinates (e.g., from the X-ray structure) and to use this information to calculate the energy of the system as a function of the atomic positions. Karplus has acknowledged the importance of major inputs in the development of the (at the time nameless) program, including
In the 1980s, finally a paper appeared and CHARMM made its public début. Gelin's program had by then been considerably restructured. For the publication, Bob Bruccoleri came up with the name HARMM (HARvard Macromolecular Mechanics), but it didn't seem appropriate. So they added a C for Chemistry. Karplus said: "I sometimes wonder if Bruccoleri's original suggestion would have served as a useful warning to inexperienced scientists working with the program."[13] CHARMM has continued to grow and the latest release of the executable program was made in August 2008 as CHARMM35b1.
The general syntax for using the program is:
charmm < filename.inp > filename.out
AMBER (an acronym for Assisted Model Building with Energy Refinement) is a family of force fields for molecular dynamics of biomolecules originally developed by the late Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields. It is maintained by an active collaboration between David Case at Rutgers University, Tom Cheatham at the University of Utah, Tom Darden at NIEHS, Ken Merz at Florida, Carlos Simmerling at Stony Brook University, Ray Luo at UC Irvine, and Junmei Wang at Encysive Pharmaceuticals.
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The term "AMBER force field" generally refers to the functional form used by the family of AMBER force fields. This form includes a number of parameters; each member of the family of AMBER force fields provides values for these parameters and has its own name.
The functional form of the AMBER force field is[1]
Note that despite the term force field, this equation defines the potential energy of the system; the force is the derivative of this potential with respect to position.
The meanings of right hand side terms are:
The form of the van der Waals energy is evinced by the equilibrium distance (σ) and well depth (ε). The factor of 2 ensures that the equilibrium distance is σ.
The form of the electrostatic energy used here assumes that the charges due to the protons and electrons in an atom can be represented by a single point charge. (Or in the case of parameter sets that employ lone pairs, a small number of point charges.)
To use the AMBER force field, it is necessary to have values for the parameters of the force field (e.g. force constants, equilibrium bond lengths and angles, charges). A fairly large number of these parameter sets exist, and are described in detail in the AMBER software user manual. Each parameter set has a name, and provides parameters for certain types of molecules.
The AMBER software suite provides a set of programs for applying the AMBER forcefields to simulations of biomolecules. It is written in Fortran 90 and C with support for most major Unix-like systems and compilers. Development is conducted by a loose association of mostly academic labs. New versions are generally released in the spring of even numbered years; AMBER 10 was released in April 2008. The software is available under a site-license agreement, which includes full source, currently priced at US$400 for non-commercial and US$20,000 for commercial organizations.
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