[gmx-users] g_hbond

[Nilesh Dhumal]

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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