[gmx-users] Re: g_hbond output

[Erik Marklund]

ZHAO Lina skrev 2011-03-16 06.33:
> @ legend length 2
> @ s0 legend "Hydrogen bonds"
> @ s1 legend "Pairs within 0.35 nm"
>          0           0           0
>        200           0           0
>        400           2           1
>        600           0           3
>        800           0           2
>       1000           1           0
>         :
>      50000           3           2
>
> Here the situations, what's the $2 and $3 mean, why when $1=1000, $3=0 
> if the $3 means pairs.
>
> I tried pymol, and on the last frame,
> there were 4 hydrogen bonds, between 7 residues. it's different from 
> here 3 2
Last time I checked there's no hbond tool in pymol (although that may 
have changed without me knowing it). I have seen scrpts that does it for 
you, but they didn't take angles into account. Hence, different criteria 
may explain the discrepancy.
>
> Thanks and sorry for last email without my realization it sent.
>
> lina


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Erik Marklund, PhD student
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