许多分子图像软件可以根据氨基酸的带电性质标记不同的颜色,但是,这样太简单了,并不代表真实的电场情况,如果要更精确的计算,需要用以下的软件:
1:GRASP(Graphical Representation and Analysis of Structural Properties)
这个是最经典的方法之一。相关信息参见:http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:GRASP
有linux和windows的版本。
2:Pymol
Pymol里面有两种方法,一是(molecule)->A(ctions)->generate->vacuum electrostatics->protein contact potential (local)
这种方法很快很方便,不过并不精确。关于这一点Pymol有一个免责声明。
二是用APBS插件来计算。Plugin->APBS tools (Adpative Poisson-Boltzmann Solver)
Click "Set grid", then "Run APBS". Finally, click on the Visualization tool, update, and click on Show Molecular Surface. You may want to select “Solvent accessible surface” and “color by potential on sol. acc. surf.” and increase the color ramp range by adjusting the high and low setpoints.
APBS采用更严格的计算,不过如果PDB中有非标准或缺失的残基就会出问题,这时必须编辑PDB文件。