[gmx-users] g_hbond

[Erik Marklund]

  Justin A. Lemkul skrev 2010-08-31 12.35:
>
>
> 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
>
It is true what Justin says. However, you can circumvent the first 
problem partialy with the -contact option. Note however that the angular 
component is lost with -contact.

Increased user control over donors and acceptors (solving problem number 
two in Justin's post) is on the wishlist, but so are many other things. 
Eventually it will be implemented, but I can't say when.
>> 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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>>
>>
>>
>


-- 
-----------------------------------------------
Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,    75124 Uppsala, Sweden
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