[gmx-users] g_hbond

[Erik Marklund]

Interesting. I can't see why that wouldn't be possible in theory, but 
there is a part of the code that would need rewriting, however.

Erik

Nilesh Dhumal skrev 2011-04-12 04.11:
> 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
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> ========================================
>>>>> --
>>>>> gmx-users mailing list    gmx-users at gromacs.org
>>>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>>>> Please search the archive at
>>>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>>>> Please don't post (un)subscribe requests to the list. Use the
>>>>> www interface or send it to gmx-users-request at gromacs.org. Can't
>>>>> post? Read
>>>>> http://www.gromacs.org/Support/Mailing_Lists
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>
>>> --
>>> -----------------------------------------------
>>> 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/
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>>> Please don't post (un)subscribe requests to the list. Use the
>>> www interface or send it to gmx-users-request at gromacs.org. Can't post?
>>> Read
>>> http://www.gromacs.org/Support/Mailing_Lists
>>>
>>>
>>>
>>>
>>
>> --
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org. Can't post? Read
>> http://www.gromacs.org/Support/Mailing_Lists
>>
>>
>>
>


-- 
-----------------------------------------------
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/