[gmx-users] g_hbond

[Erik Marklund]

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/