[gmx-users] g_hbond

[Nilesh Dhumal]

I tried to use contact and -da together with following  command

g_hbond -f 3.trr -s 3.tpr -n hbond19.ndx -nonitacc   -noda   -r 0.5
-contact   -num

I am getting following error.

Fatal error:Can not analyze contact between H and A: turn off -noda

Nilesh



On Mon, April 11, 2011 5:05 pm, Nilesh Dhumal wrote:
> 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
>> phone:    +46 18 471 4537        fax: +46 18 511 755
>> erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/
>>
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>
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