[gmx-users] Gmx hbond

farial tavakoli farial.tavakoli at ymail.com
Sun Aug 6 22:32:06 CEST 2017

 blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Hi justin
Thank you for your replyingBut you said in this tuturial, in order to have tc_groups = protein non-protein , it is best to consider protein and ligand as one single entity. So we use make-ndx to merg them. When i issue gmx hbond there isnt any ligand in this list to choose. How can i determine h bonds between protein and ligan , even in my project that is about HDAC2 and my designed drug
Thank you Farial

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On Sunday, August 6, 2017, 5:06 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

On 8/4/17 11:13 AM, farial tavakoli wrote:
>  blockquote, div.yahoo_quoted { margin-left: 0 !important; border-left:1px #715FFA solid !important; padding-left:1ex !important; background-color:white !important; }  Dear gromacs user
> I am performing protein ligand complex (t4lysosim) and now i need to analyze JZ4 hydrogen bonding, but when i type Gmx hbondThere is no JZ4 in the list to choose. It is because of i used :Gmx make_ndx -f em.gro -o index.ndxAnd merged the " protein " and " JZ4" groupsIs there anyone help me how to check the hydrogen bond of JZ4 ligand?

Both protein and ligand are default groups and do not require the use of an 
index file.  If the ligand isn't showing up in the list, it's probably because 
you're supplying an index file from which the ligand group has been deleted.



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

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