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

[David van der Spoel]

On 01/08/17 04:15, yujie Liu wrote:
> 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.

You do not mention what problem you are encountering, but any way, you 
are probably wasting your time with implicit solvents, including PBSA. 
My recent paper is one in a long row of papers that explain why the 
results are very poor.
http://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00169
> 
> 
> Yours sincerely
> 
> Yujie, liu
> 


-- 
David van der Spoel, Ph.D., Professor of Biology
Head of Department, Cell & Molecular Biology, Uppsala University.
Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
http://www.icm.uu.se