The most important question to ask now is why choose 1.2 nm? The short answer is that you don't want the protein to 'see' its periodic image across the boundary of the box. If you refer to the original paper for the AMBER 03 force field (Duan, et al., J. Comput ...
autoimage(Automatically re-image coordinates 坐标自动重新成像) Automatically center and image (by molecule) a trajectory with periodic boundaries. For most cases just specifying’autoimage’ alone is sufficient. The ’anchor’ molecule (default the first molecule) will be centered; all’fix ...
scee静电比例常数,默认值1.2;scnb范德华比例常数,默认值2.0。一般不需要更改,注意!Amber11之后这两个参数只在拓扑文件中产生,而不在Sander中运行了。 scee Usage: scee value Allows the user to set/change the value of the electrostatic scaling constant that will be used to scale 1-4 electrostati ...
对于带有电荷的小分子,在使用 antechamber计算电荷的时候,需要使用 -nc flag,具体用法见下面语句,以下内容转载自amber QA http://archive.ambermd.org/201010/0417.html If the molecule is charged in the system of interest, please use the -nc flag with antechamber as in ...