[gmx-users] Gmx hbond

[Justin Lemkul]

On 8/6/17 4:21 PM, 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; }  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 

...for the purpose of thermostatting, nothing else.  Again, merging two groups 
doesn't eliminate either from the list unless you actually deleted them.

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

If you're working on a different system, you're not going to have the exact same 
options as in my tutorial.  Likely your ligand isn't called "JZ4," so look for 
something else that makes sense for your system.

-Justin

> Thank you Farial
> 
> 
> 
> Sent from Yahoo Mail for iPhone
> 
> 
> 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
> 

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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