[gmx-users] about g_hbond

[lina]

On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> lina wrote:
>>
>> Hi,
>>
>> For group A, b, C.
>>
>> It's no doubt can get hb forming number between A-b, b-C. b-(A or C).
>>
>> But I don't know how to get the number of residues of b forming both
>> with A and B at the same time. namely b-A&C, not with AC group.
>>
>
> There's no direct way to do it, but from the output files of g_hbond it can
> be done.  You'd need the .xpm files of A-C and B-C hydrogen bonds, and write
> some script that parses the .xpm files, and whenever there is an entry of
> A-C in the same frame as B-C, then you have a hydrogen bond mediated between
> the two. There's lots of discussion in the list archive about water-mediated
> hydrogen bonds that is likely applicable here.

Thanks, I will try.

>
> Note that if you're using g_hbond in version 4.5, there is an important bug
> that was fixed just yesterday:
>
> http://lists.gromacs.org/pipermail/gmx-users/2011-May/061249.html

I noticed yesterday and recompiled the gromacs already. Thanks for reminding.

>
> -Justin
>
>> Thanks,
>> --
>> Best Regards,
>>
>> lina
>>
>>
>>
>
> --
> ========================================
>
> 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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-- 
Best Regards,

lina