[gmx-users] g_hbond

[Nilesh Dhumal]

Is it possible to find number of hydrogen bonds using g_hbond by
considering the distance between Acceptor-hydrogen instead of the distance
between Acceptor-Donor atoms.

Nilesh

On Mon, April 11, 2011 3:32 pm, Erik Marklund wrote:
> Try the -contact option.
>
>
> Erik
>
>
>
> Nilesh Dhumal skrev 2011-04-11 17.12:
>
>> Is there any way to specify clorin and florin atoms as a receptor.
>>
>>
>> Nilesh
>>
>>
>> On Mon, April 11, 2011 11:08 am, Justin A. Lemkul wrote:
>>
>>> Nilesh Dhumal wrote:
>>>
>>>
>>>> Hello,
>>>>
>>>>
>>>>
>>>> I am trying to calculate number of hydrogen bond (O-H---CL)in my
>>>> system.
>>>>
>>>> I use the following command
>>>>
>>>>
>>>>
>>>>
>>>> g_hbond -f 3.trr -s 3.tpr -n hbond18.ndx -nonitacc -num
>>>>
>>>>
>>>> Output file hbnum.xvg shows zero number of hydorgen bond.
>>>>
>>>>
>>>>
>>>> Can you tell me why its showing zero no.
>>>>
>>>>
>>>>
>>>> A strong peak is found in rdf between H and CL at 2.0 A.
>>>>
>>>>
>>>>
>>> Chlorine is not considered a receptor in g_hbond.
>>>
>>>
>>>
>>> -Justin
>>>
>>>
>>>
>>>> I am using Gromacs 4.0.7 version.
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> 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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> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
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