[gmx-users] Re: g_hbond output

[Erik Marklund]

Erik Marklund skrev 2011-03-16 16.25:
> 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.
I should add that there are issues with the current version of g_hbond, 
and I'm trying to find the time to fix them, but I'm in the process of 
finalizing my thesis, so I won't do it right away.
>>
>> Thanks and sorry for last email without my realization it sent.
>>
>> lina
>
>


-- 
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Erik Marklund, PhD student
Dept. of Cell and Molecular Biology, Uppsala University.
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erikm at xray.bmc.uu.se    http://folding.bmc.uu.se/