[gmx-users] about g_hbond
lina.lastname at gmail.com
Wed May 11 17:15:23 CEST 2011
On Wed, May 11, 2011 at 11:10 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> lina wrote:
>> 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:
I noticed yesterday and recompiled the gromacs already. Thanks for reminding.
>> Best Regards,
> 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
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