[gmx-users] g_mindist

[Justin A. Lemkul]

ahmet yıldırım wrote:
> Dear Justin,
> 
> can you suggest me published paper related to about hydrophobic and 
> hydrophilic contacts?
> 

A few minutes on Google or the literature searching database of your choice 
should turn up something useful.  If you need to understand the definition or 
nature of such interactions, a basic biochemistry textbook should cover it.

-Justin

> 03 Temmuz 2011 00:24 tarihinde Justin A. Lemkul <jalemkul at vt.edu 
> <mailto:jalemkul at vt.edu>> yazdı:
> 
> 
> 
>     ahmet yıldırım wrote:
> 
>         Dear Justin,
> 
>         You said before "you can obtain some idea by using g_mindist to
>         calculate hydrophobic and hydrophilic contacts between the
>         protein and ligand".
> 
>         That is, I can explore whether there is hydrophobic or
>         hydrophilic feature of ligand using g_mindist tool. is this correct?
>         I did the calculations related to protein_ligand interactions
>         (protein contains two ligand). I plotted the graphs of distance
>         and numcount versus simulation time for each ligand. The number
>         of contacts in  ligand x is more than the other ligand y. Which
>         of this ligands are hydrophobic? Which is hydrophilic? I know
>         you are not private tutor. Please don't be angry :(
> 
> 
>     I certainly hope I haven't given the impression that I'm some angry
>     tyrant.  I'm happy to answer reasonable questions across the list,
>     time permitting.
> 
>     To obtain information about hydrophobic and hydrophilic contacts,
>     you need to use special index groups that tell g_mindist (or any
>     other tool) which atoms to consider.  In this way, you can count how
>     many of each type of contact evolve over time.
> 
>     -Justin
> 
>     -- 
>     ==============================__==========
> 
>     Justin A. Lemkul
>     Ph.D. Candidate
>     ICTAS Doctoral Scholar
>     MILES-IGERT Trainee
>     Department of Biochemistry
>     Virginia Tech
>     Blacksburg, VA
>     jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
>     http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin
>     <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> 
>     ==============================__==========
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> 
> 
> -- 
> Ahmet YILDIRIM

-- 
========================================

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

========================================