[gmx-users] It is protein and ligand...Fwd: Protein-Ligand Complex MD simulation : Number of Hydrogen bond ; Options to Choose

[Adarsh V. K.]

Dear Mark,

Happy to see the response. I need clarification on...The hydrogen bond
between protein and ligand. Generally for drug discovery we use H bond
between protein side chain and ligand. But it is not clear from gromacs
documentation what options to choose after issuing a

gmx hbond...... command

After the command and the screen display options to choose,

Which option I have to choose for the hydrogen bond between *protein and
ligand?.*

protein

protein-H

side chain

side chain-H

---------- Forwarded message ----------
From: Adarsh V. K. <adarsh_p130085bt at nitc.ac.in>
Date: Wed, Jan 25, 2017 at 2:18 PM
Subject: Protein-Ligand Complex MD simulation : Number of Hydrogen bond ;
Options to Choose
To: gromacs.org_gmx-users-request at maillist.sys.kth.se, gmx-users at gromacs.org


Dear all,

Protein-ligand complex MD simulation using Gromacs 5.1.4 (Drug discovery)

Can you please tell me command for Number of Hydrogen bond plot?

It is # gmx hbond...

But what option we have to choose, apart from Ligand (13)

Is it (option after the command),

protein

protein-H

side chain

side chain-H

Regards,
Adarsh V. K.