[gmx-users] Some problem about the process of calculating MM-PBSA binding free energy

[yujie Liu]

Dear users;

I met some problem when I calculated the binding free energy between
protein and ligand by the g_mmpbsa program. I am sure that I had read the
tutorials of its official website and some other related information, but I
don’t know what should I set the value of pconc or nconc in the input
parameter when I use the file of polar.mdp. The default value is 0.150.
Also, I don’t add fixed concentration when I use gmx genion  command by
GROMACS program and only use -neutral option.


Yours sincerely

Yujie, liu