amber中frcmod,mol2文件的格式

一、mol2文件格式

二、Frcmod文件格式：

http://ambermd.org/formats.html

举例：

remark goes here      #用于识别参数设置的标题

MASS   #原子标志和原子质量（1 , 2, 3）

Mg 24.000         0.000               ATTN, need revision

1、原子名称 （The unique atom symbol used in the system.）

2、原子质量（Atomic mass of the center having the symbol "KNDSYM"）

3、原子极化度（The atomic polarizability for each atom (in A**3) This is the type of polarizability used in sander and gibbs. No parameters are supplied for this since the feature is still in development(Amber 4.1).）

BOND（IBT , JBT , RK , REQ）

Mg-nd  600.00   2.000       ATTN, need revision

Mg-nf  600.00   2.070       ATTN, need revision

IBT-JBT：（成键原子）Atom symbols for the two bonded atoms.

RK：（力常数）The harmonic force constant for the bond "IBT"-"JBT".The unit is kcal/mol/(A**2).

REQ：（平衡键长）The equilibrium bond length for the above bond in Angstroms 

ANGLE   （ITT , JTT , KTT , TK , TEQ）

Mg-nd-cc   90.000     128.000   ATTN, need revision

Mg-nd-cd   90.000     122.000   ATTN, need revision

ce-cf-nf   70.110     118.320   same as c2-cf-nf

ITT-JTT-KTT：成键角原子 （The atom symbols for the atoms making an angle.）

TK：键角力常数（The harmonic force constants for the angle "ITT"-"JTT"- "KTT" in units of kcal/mol/(rad**2) (radians are the traditional unit for angle parameters in force fields).）

TEQ：平衡键角（The equilibrium bond angle for the above angle in degrees.）

DIHE  （IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN）

ce-ce-nf-cf   1    4.150       180.000           2.000      same as X -c2-nf-X

IPT-JPT-KPT-LPT：成二面角原子（The atom symbols for the atoms forming a dihedral angle. If IPT .eq. 'X ' .and. LPT .eq. 'X ' then any dihedrals in the system involving the atoms "JPT" and and "KPT" are assigned the same parameters. This is called the general dihedral type and is of the form "X "-"JPT"-"KPT"-"X ".）

IDIVF：二面角势垒分为几个（The factor by which the torsional barrier is divided. Consult Weiner, et al., JACS 106:765 (1984) p. 769 for details. Basically, the actual torsional potential is (PK/IDIVF) * (1 + cos(PN*phi - PHASE))）

PK：势垒/2

PHASE：相转换角度

PN：二面角势垒的周期性

IMPROPER（IPT , JPT , KPT , LPT , IDIVF , PK , PHASE , PN）

c3-cd-ce-ce         1.1          180.0         2.0          Using default value

与二面角项一样，只不过没有IDIVF项。（The input is the same as in for the dihedrals except that the torsional barrier height is NOT divided by the factor idivf. The improper torsions are defined between any four atoms not bonded (in a successive fashion) with each other as in the case of "regular" or "proper" dihedrals. Improper dihedrals are used to keep certain groups planar and to prevent the racemization of certain centers in the united atom model. Consult the above reference for details.）

NONBON  （LTYNB , R , EDEP）

  Mg          0.0000  0.0000             ATTN, need revision

LTYNB：原子

R：范德华半径

EDEP：井深（The 6-12 potential well depth. (kcal/mol)）