[gmx-users] Docking using MDS

[Justin A. Lemkul]

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vivek sharma wrote:
> Hi justin,
> Thanks for your reply...
> Actually I tried docking with autodock, but I am not happy with the 
> results I am getting, they are not showing the expected energy value and 
> interaction as reported in literature.

Well, then the first thing to look for is orientation.  If AutoDock did not 
produce the right orientations for your ligands, *maybe* MD will.  Visual 
inspection would be the most immediate thing to do.

Any other forms of analysis would be dependent upon your system.  Do your 
ligands form H-bonds with the amino acids of your receptor (g_hbond)?  Do 
contacts within the protein change, and/or what contacts between the ligand and 
protein result (g_mdmat)?

Other than that, read the descriptions of the analysis tools, maybe they will 
inspire you :)

-Justin

> So, I want to try docking using MDS(to study ligand binding by MD) as 
> well as scoring docked results using MDS (running MD on docked 
> configurations).
> 
> And I am having no clue for the same, any suggestion or guidance would 
> be of great help.
> 
> With Thanks,
> Vivek
> 
> 2008/10/1 Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> 
> 
> 
>     vivek sharma wrote:
> 
>         Hi There,
> 
>         I am trying to run MD simulation for screening  my docking
>         result, but I am not aware of what are the parameters and
>         analysis we can do for docking by using MD simulation.
> 
> 
>     That depends entirely upon the scope of your question and what you
>     want to learn.  Are you running MD on docked configurations, or are
>     you trying to study ligand binding by MD?
> 
>     What is it that you are trying to investigate?  This question will
>     largely motivate what type of analysis you do.
> 
>     -Justin
> 
>         If anybody have tried the similiar things using GROMACS, Please
>         help me in this regard.
> 
> 
> 
>         With Thanks,
>         VIvek
> 
> 
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> 
>     -- 
>     ========================================
> 
>     Justin A. Lemkul
>     Graduate Research Assistant
>     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
> 
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> 

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

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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