[gmx-users] Using g_mindist for calculating hydrophobic interaction between protein and ligand

[Agnivo Gosai]

Dear Users

I wish to characterize the hydrophobic interactions between a protein and a
ligand by using the g_mindist analysis tool.
I searched the forum and found a post which tells that it is supposedly the
best tool available in gromacs for doing the job.
Now , while reading the post a doubt cropped up in my mind.
Do I need to provide an index file containing only the hydrophobic residues
of the protein and the ligand ?
Or, just a normal index file with all the protein residues and ligand
residues in two separate groups will do the job?


Thanks & Regards
Agnivo Gosai
Grad Student, Iowa State University.