[gmx-users] Re: Hbonds - Res - Ligand

[Justin A. Lemkul]

Steven Neumann wrote:
> Hi Justin,
>  
> Do you have any clue of this problem? You are the last hope, please help :)
>  

Sorry, I have no idea.  If I did, I would have posted earlier.  In principle, 
PBC re-imaging should not affect the calculation of distances and angles needed 
by g_hbond and I have never seen such an outcome.

-Justin

> Steven
> 
> On Fri, Oct 28, 2011 at 2:45 PM, Steven Neumann <s.neumann08 at gmail.com 
> <mailto:s.neumann08 at gmail.com>> wrote:
> 
>     With other residues is the same... and changes are bigger. Which
>     trajectory in this case is reliable?
>      
>     My wsteps in trjconv involves:
>      
> 
>     1.      First make your molecules whole if you want them whole (system).
> 
>      
> 
>     3.      Extract the first frame from the trajectory as reference for
>     removing jumps if you want to remove jumps.
> 
>      
> 
>     4.      Remove jumps if you want to have them removed using the
>     first frame
> 
>      
> 
>     5.      Center your system using some criterion. Doing so shifts the
>     system, so don't use |trjconv -|pbc| nojump| after this step.
> 
>      
> 
>     6.      Put everything in some box.
> 
>      
> 
>     7.      Fit if desired and don't use any PBC related option afterwards.
> 
>      
> 
> 
>     On Fri, Oct 28, 2011 at 2:28 PM, Steven Neumann
>     <s.neumann08 at gmail.com <mailto:s.neumann08 at gmail.com>> wrote:
> 
>         Dear Gmx Users,
>          
>         I have compared average number of hbonds per time frame between
>         my ligand and protein:
>          
>         1) Using trajectory obtained straight after simulations:
>          
>         g_hbond -f md2.trr -s md2.tpr -n SystemGRP.ndx -num
>         91withLigandsHbond.xvg
>          
>         Avergage number of hbonds: 0.146
>          
>         2) Using trajectory modified by trjconv according to the PBC
>         workflow on www.gromcacs.org <http://www.gromcacs.org/> :
>          
>         g_hbond -f md2final2.xtc -s md2.tpr -n SystemGRP.ndx -num
>         91withLigandsHbond.xvg
>          
>         Avergage number of hbonds: 0.156
> 
>         Does anyone know why this value changed and I obtained slightly
>         different results?
> 
>         Thank you,
> 
>         Steven
> 
> 
> 

-- 
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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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