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

[Justin Lemkul]

On 1/26/17 4:47 AM, Adarsh V. K. wrote:
> 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?.*
>

See manual section 8.1.1 to learn what all of these are.

-Justin

> 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.
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================