『讨论』做分子对接的朋友们：在autodock4中配体和受体默认八种原子类型，如何才能修改源代码可以计算Cl和Br！我按照手册里说的加入AD4_prameter.dat命令，结果还是不行，怎么才能认Cl和Br啊？先谢谢大家了
把我的gpf文件拷在这里，大家看看有什么问题吗？
parameter_file AD4_parameters.dat                    
npts 126 126 100                     # num.grid points in xyz
gridfld Kir.maps.fld                 # grid_data_file
spacing 0.375                        # spacing(A)
receptor_types A C HD N NA OA SA     # receptor atom types
ligand_types A NA C HD N Cl          # ligand atom types
receptor Kir.pdbqt                   # macromolecule
gridcenter -3.877 0.229 -0.674       # xyz-coordinates or auto
smooth 0.5                           # store minimum energy w/in rad(A)
map Kir.A.map                        # atom-specific affinity map
map Kir.NA.map                       # atom-specific affinity map
map Kir.C.map                        # atom-specific affinity map
map Kir.HD.map                       # atom-specific affinity map
map Kir.N.map                        # atom-specific affinity map
map Kir.Cl.map                       # atom-specific affinity map
elecmap Kir.e.map                    # electrostatic potential map
dsolvmap Kir.d.map                   # desolvation potential map
dielectric -0.1465                   # <0, AD4 distance-dep.diel;>0, constant
按照前面的帖子：
1、编译autodock3/4前，编辑autodock/autocomm.h，修改下面的数值：
        #define MAX_MAPS     14  
        #define ATOM_MAPS    12  
注：
        MAX_MAPS：Maximum number of energy maps.（默认8）
        ATOM_MAPS：Number of atomic affinity grids.（默认6）

2、编译AutoGrid3之前，编辑autogrid/autocomm.h，修改下面的数值：
        #define MAX_MAPS     14  
        #define ATOM_MAPS    12  
注：
        MAX_MAPS：Maximum number of energy maps.（默认8）
        ATOM_MAPS：Number of atomic affinity grids.（默认6）

3、autogrid4的编译，不需要修改。
修改后还是算得不对啊！！！
[search]autodock4[/search]

[ Last edited by zhlrui on 2008-4-16 at 20:42 ]

How do I add new atom types?

Important: Bear in mind that the AutoDock 4 scoring function was calibrated for the current set of atom types, and that if you add new ones, strictly speaking you should perform a re-calibration of the force field to determine the correct coefficients for the molecular mechanics terms and the empirical term of the linear free energy model.

You will need to find, compute or set the following values for each new atom type, which you specify after the "atom_par" keyword. Note that the values on each "atom_par" line are space delimited, not fixed width. You will need to add one "atom_par" line for every new atom type. It is possible to define 'synonyms' for atom types, by repeating the numerical atom parameter lines for every variant of the atom type's one- or two-character name.

    * name of the atom type; this can be one or two characters long, and should correspond to the atom type at the end of ATOM or HETATM lines in PDBQT files; specify this in the "Atom Type" field
    * van der Waals radius of the atom/ion (in Angstrom); specify twice this value in the "Rii" field
    * epsilon or energy well depth for two like interacting atoms/ions (in Kcal/mol); specify in the "epsii" field
    * volume of the atom/ion (in Angstrom^3); compute this from 4/3 * PI * (Rii/2)^3; specify in the "vol" field
    * atomic solvation parameter of the atom/ion; the ai or "ASP" values in the equation for Si in the description of the Desolvation Free Energy Term in AutoDock 4; specify this in the "solpar" field
    * hydrogen bonding radius (in Angstrom); for non-hydrogen-bonding atom types this is 0.0; specify this in the "Rij_hb" field
    * hydrogen bonding energy well depth (in Kcal/mol); for non-hydrogen-bonding atom types this is 0.0; specify this in the "epsij_hb" field
    * hydrogen bonding type; an integer; for non-hydrogen-bonding atom types this is 0; specify this in the "hbond" field
    * receptor type index; an integer; default value is -1; specify this in the "rec_index" field
    * grid map index; an integer; default value is -1; specify this in the "map_index" field
    * bond type index; an integer; default value is 4; specify this in the "bond_index" field

The last six values (0.0 0.0 0 -1 -1 4) will be the same if the atom type is not involved in hydrogen bonding.

Note that a comment can be specified after a number sign symbol, #

Remember to use the "parameter_file AD4_parameters.dat" command in both the GPF and DPF, so that the new parameters are used in both the AutoGrid pre-calculation of the grid maps, and in the AutoDock dockings. Specify this command on the first line of the GPF and DPF files.

谢谢了，我刚刚开始用autodock4，很多问题不懂啊，能不能用中文跟俺讲讲？在ADT里修改参数还是在脚本里？

这段话出自哪里啊？我要加的原子类型不是新的，是较为常见的Cl和Br啊

是说如果你加的原子 在AUTODOCK里面没有的话  就要自己添加了

可是如何加啊？我查了一些资料但是由于对程序还不是很熟不知从何下手啊！如果能解决的话，那真是太感谢你了;)，我的qq76098572，可以和你讨论吗？

大家没有做过的啊？这几天一直在解决上述问题，头发都要愁白了！！！:P

楼主，我也刚开始学AUTODOCK4，有空我们讨论一下吧，我的QQ是330675050，：）

楼主，我也刚开始学AUTODOCK4,应该建一个Autodock专区哦，呵呵

帮你顶一下。:D

多谢大家没让帖子沉了，我的问题已经困扰我半个月多了，最近尝试了不少方法还是没有解决，大家帮忙献计献策啊！

又试了几种方法还是没有解决，郁闷中！

谢谢大家，我的问题已经解决，是在配体的pdbqt文件里把原子类型改对了就行了！