[gmx-users] g_hbond

[Justin A. Lemkul]

Nilesh Dhumal wrote:
> THanks.
> I have one more system dioxin + water molecules. There is possiblity of
> C-H---O hydrogen bond. The CH bond of dioxin and oxygen atom of water.
> I want to calculate the number of hydrogen  bonds.
> I used the following command
>  g_hbond -f dix-bdmp.trr -s dix-bdmp.tpr -n dix-bdmp-no.ndx -num
>  I selected the hydrogen atom and oxygen atom of water
> 
> Igot this error
> Checking for overlap in atoms between H96 and O21
> Calculating hydrogen bonds between H96 (4 atoms) and O21 (256 atoms)
> Found 0 donors and 256 acceptors
> No Donors found
> 
> -------------------------------------------------------
> Program g_hbond, VERSION 4.0.5
> Source code file: gmx_hbond.c, line: 2235
> 
> Fatal error:
> Nothing to be done
> 

Two problems:

1. As g_hbond states, you don't have any donors.  It is insufficient to supply 
only H atoms in the "donor" group, since g_hbond needs to calculate geometric 
parameters related to the D-H...A angle, so the heavy atom to which the H is 
connected must be included in this group as well.

2. I don't believe g_hbond will recognize any hydrogen bonds involving CH species.

-Justin

> Nilesh
> 
> On Mon, August 30, 2010 10:47 pm, Justin A. Lemkul wrote:
> 
>> Nilesh Dhumal wrote:
>>
>>> Hello,
>>> I have a system with a glucose molecule and 256 water molecules.
>>> I want to find out the number of hydrogen bond between the hydrogen atom
>>>  of OH group of glucose and the oxygen atom of water. How can I  make
>>> the index file.
>> Type "help" at the make_ndx prompt for examples.  These groups are very
>> easy to create by specifying the desired atom names.
>>
>> -Justin
>>
>>
>>> Thanks
>>>
>>>
>>> NIlesh
>>>
>>>
>>>
>>>
>> --
>> ========================================
>>
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>
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> 
> 
> 

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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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