gromac如何计算大分子结构之间的interaction energy

Jonaldlow

大家好，

   我是马来西亚人，生物领域的本科生，刚接触gromac，想计算antigen（病原）和 receptor 直接的interaction energy，但antigen分子太大，做ligand topology的时候会出现error。目前我是把antigen和 receptor combine成为一个pdb file做protein topology， 但计算出来的rmsd和interaction energy都不大理想， 是不是因为计算出来的是energy是属于whole system的，而不是antigen和receptor之间的interaction energy，后者要如何执行呢？ 如果有什么我理解错误的地方，请务必纠正我。谢谢。

student0618

1. For the RMSD you better use gmx trjconv to handle periodic boundary condition first. You may need to use -pbc cluster for the two big molecules.
2. For the antigen, if it's a protein just use the protein forcefield.
3. Provide more details on what exactly you have done when you calculate the interaction energy, "不太理想" is not specific enough. There are several ways to calculate, depends on the type of system some maybe more preferable than others.