[gmx-users] g_hbond

[Nilesh Dhumal]

THanks.
I have one more system dioxin + water molecules. There is possiblity of
C-H---O hydrogen bond. The CH bond of dioxin and oxygen atom of water.
I want to calculate the number of hydrogen  bonds.
I used the following command
 g_hbond -f dix-bdmp.trr -s dix-bdmp.tpr -n dix-bdmp-no.ndx -num
 I selected the hydrogen atom and oxygen atom of water

Igot this error
Checking for overlap in atoms between H96 and O21
Calculating hydrogen bonds between H96 (4 atoms) and O21 (256 atoms)
Found 0 donors and 256 acceptors
No Donors found

-------------------------------------------------------
Program g_hbond, VERSION 4.0.5
Source code file: gmx_hbond.c, line: 2235

Fatal error:
Nothing to be done

Nilesh

On Mon, August 30, 2010 10:47 pm, Justin A. Lemkul wrote:
>

>
> Nilesh Dhumal wrote:
>
>> Hello,
>> I have a system with a glucose molecule and 256 water molecules.
>> I want to find out the number of hydrogen bond between the hydrogen atom
>>  of OH group of glucose and the oxygen atom of water. How can I  make
>> the index file.
>
> Type "help" at the make_ndx prompt for examples.  These groups are very
> easy to create by specifying the desired atom names.
>
> -Justin
>
>
>> Thanks
>>
>>
>> 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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