[gmx-users] g_hbond tool question

Carlos Navarro Retamal cnavarro at utalca.cl
Wed Nov 19 13:58:41 CET 2014


Dear Erik,
Thanks for your replay.
You are right.
I was looking into: http://www.gromacs.org/Documentation/Terminology/Default_Index_Groups and i found that i misunderstood the description of the groups.
According to the documentation, ‘sidechains-H' correspond to all the atoms of the sidechain EXCEPT the hydrogen atoms.
So in that case, with the option
‘sidechain' + 'MainChain+H’ i got the same values that i got with ‘Protein’ (the whole protein)
Thanks a lot!,
Kind regards,
Carlos


--  
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics and Molecular Simulations (CBSM)
Universidad de Talca
2 Norte 685, Casilla 721, Talca - Chile   
Teléfono: 56-71-201 798,  
Fax: 56-71-201 561
Email: carlos.navarro87 at gmail.com or cnavarro at utalca.cl


On Wednesday, November 19, 2014 at 6:18 AM, Erik Marklund wrote:

> Dear Carlos,
>  
> You get a double contribution from MainChain and SideChain in this way, don't you?
>  
> Kind regards,
> Erik
>  
> On 19 Nov 2014, at 03:00, Carlos Navarro Retamal <cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)> wrote:
>  
> > Dear gromacs users,  
> > I’m studying the hydrogen bond interaction between a protein and different solvents.To do that i’m using the g_hbond tools of gromacs (4.6.3 version).
> > As groups,I started using ‘Protein’ and ‘Sol’ and i got an specific number.
> > After that, to analyse the interaction in a more specific way between this 2 groups, i ran the g_hbond tools using different groups:
> > 'MainChain+Cb' - 'SOL'
> > 'MainChain+H' - ‘SOL'
> > 'SideChain' - 'SOL'
> > 'SideChain+H’ - ‘SOL’
> > But when i sum hbond got by these four selections i got different values (higher) than the values got from ‘Protein’ - ‘SOL’
> > Why is this happening? Am i interpreting in a wrong way what the selection ‘Protein’ - ‘SOL’ is considering?
> > Hope someone can help me.
> > Thanks in advances,
> > Carlos
> >  
> >  
> > --  
> > Carlos Navarro Retamal
> > Bioinformatic engineer
> > Ph.D(c) in Applied Science, Universidad de Talca, Chile
> > Center of Bioinformatics and Molecular Simulations (CBSM)
> > Universidad de Talca
> > 2 Norte 685, Casilla 721, Talca - Chile  
> > Teléfono: 56-71-201 798,  
> > Fax: 56-71-201 561
> > Email: carlos.navarro87 at gmail.com (mailto:carlos.navarro87 at gmail.com) or cnavarro at utalca.cl (mailto:cnavarro at utalca.cl)
> >  
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