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。

[编辑] 构成

一般而言，分子力场函数由以下几个部分构成：

• 键伸缩能：构成分子的各个化学键在键轴方向上的伸缩运动所引起的能量变化
• 键角弯曲能：键角变化引起的分子能量变化
• 二面角扭曲能：单键旋转引起分子骨架扭曲所产生的能量变化
• 非键相互作用：包括范德华力、静电相互作用等与能量有关的非键相互作用
• 交叉能量项：上述作用之间耦合引起的能量变化

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。

[编辑] 常用力场函数和分类

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

• 传统力场
  • AMBER力场：由Kollman课题组开发的力场，是目前使用比较广泛的一种力场，适合处理生物大分子。
  • CHARMM力场：由Karplus课题组开发，对小分子体系到溶剂化的大分子体系都有很好的拟合。
  • CVFF力场：CVFF力场是一个可以用于无机体系计算的力场
  • MMX力场：MMX力场包括MM2和MM3，是目前应用最为广泛的一种力场，主要针对有机小分子
• 第二代力场

  第二代的势能函数形式比传统力场要更加复杂，涉及的力场参数更多，计算量也更大，当然也相应地更加准确。

  • CFF力场CFF力场是一个力场家族，包括了CFF91、PCFF、CFF95等很多力场，可以进行从有机小分子、生物大分子到分子筛等诸多体系的计算
  • COMPASS力场由MSI公司开发的力场，擅长进行高分子体系的计算
  • MMF94力场Hagler开发的力场，是目前最准确的力场之一
• 通用力场

  通用力场也叫基于规则的力场，它所应用的力场参数是基于原子性质计算所得，用户可以通过自主设定一系列分子作为训练集来生成合用的力场参数

  • ESFF力场MSI公司开发的力场，可以进行有机、无机分子的计算
  • UFF力场可以计算周期表上所有元素的参数
  • Dreiding力场适用于有机小分子、大分子、主族元素的计算

编辑	分子力场
传统力场 AMBER力场 - CHARMM力场 - CVFF力场 - MMX力场 第二代力场 CFF力场 - COMPASS力场 - MMFF94力场 通用力场 ESFF力场 - UFF力场 - Dreiding力场

CHARMM

From Wikipedia, the free encyclopedia

CHARMM

Developer(s)	Martin Karplus, Accelrys
Initial release	1983 (1983)
Stable release	c35b3 / 2009-08-15; 4 months ago
Preview release	c36a3 / 2009-08-15; 4 months ago
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.

Contents [hide] 1 CHARMM force fields 2 CHARMM molecular dynamics program 3 History of the program 4 Running CHARMM Under Unix/Linux 5 CHARMM and Volunteer Computing 6 See also 7 References 8 External links

[edit] CHARMM force fields

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.

[edit] CHARMM molecular dynamics program

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.

[edit] History of the program

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

• Schneior Lifson's group at the Weizmann Institute, especially from Arieh Warshel who went to Harvard and brought his consistent force field (CCF) program with him;
• Harold Scheraga's group at Cornell University; and
• Awareness of Michael Levitt's pioneering energy calculations for proteins

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.

[edit] Running CHARMM Under Unix/Linux

The general syntax for using the program is:

charmm < filename.inp > filename.out

charmm 

The actual name of the program (or script which runs the program) on the computer system being used.

filename.inp 

A text file which contains the CHARMM commands. It starts by loading the molecular topologies (top) and force field (par). Then one loads the molecular structures' Cartesian coordinates (e.g. from PDB files). One can then modify the molecules (adding hydrogens, changing secondary structure). The calculation section can include energy minimization, dynamics production, and analysis tools such as motion and energy correlations.

filename.out 

The log file for the CHARMM run, containing echoed commands, and various amounts of command output. The output print level may be increased or decreased in general, and procedures such as minimization and dynamics have printout frequency specifications. The values for temperature, energy pressure, etc. are output at that frequency.

AMBER

From Wikipedia, the free encyclopedia

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.

Contents [hide] 1 Force field 1.1 Functional form 1.2 Parameter sets 2 Software 2.1 Programs 3 See also 4 References 4.1 Further reading 5 External links

[edit] Force field

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.

[edit] Functional form

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:

• First term (summing over bonds): represents the energy between covalently bonded atoms. This harmonic (ideal spring) force is a good approximation near the equilibrium bond length, but becomes increasingly poor as atoms separate.
• Second term (summing over angles): represents the energy due to the geometry of electron orbitals involved in covalent bonding.
• Third term (summing over torsions): represents the energy for twisting a bond due to bond order (e.g. double bonds) and neighboring bonds or lone pairs of electrons. Note that a single bond may have more than one of these terms, such that the total torsional energy is expressed as a Fourier series.
• Fourth term (double summation over i and j): represents the non-bonded energy between all atom pairs, which can be decomposed into van der Waals (first term of summation) and electrostatic (second term of summation) energies.

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.)

[edit] Parameter sets

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.

• Peptide, protein and nucleic acid parameters are provided by parameter sets with names beginning with "ff" and containing a two digit year number, for instance "ff99".
• GAFF (Generalized AMBER force field) provides parameters for small organic molecules to facilitate simulations of drugs and small molecule ligands in conjunction with biomolecules.
• The GLYCAM force fields have been developed by Rob Woods for simulating carbohydrates.

[edit] Software

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.

[edit] Programs

• LEaP is used for preparing input files for the simulation programs
• Antechamber automates the process of parameterizing small organic molecules using GAFF
• SANDER (Simulated Annealing with NMR-Derived Energy Restraints) is the central simulation program and provides facilities for energy minimization and molecular dynamics with a wide variety of options
• pmemd is a somewhat more feature-limited reimplementation of sander by Bob Duke. It was designed with parallel processing in mind and has significantly better performance than sander when running on more than 8–16 processors
• nmode calculates normal modes
• ptraj provides facilities for numerical analysis of simulation results. AMBER does not include visualization capabilities; visualization is commonly performed with VMD. A new visualization alternative is Sirius.
• MM-PBSA allows for implicit solvent calculations on snap shots from molecular dynamics simulations

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