[gmx-developers] Request for information about docking in gromacs

[David van der Spoel]

Subramanian Arun Kumar wrote:
> Dear all,
> 
> I am a postdoc in Computational Chemistry at the Denmark Technical 
> University (doing most of my MD applications with NAMD). I am very much 
> interested to participate in contributing to Gromacs development. After 
> looking at the volunteer titles posted in the GMX developers page, I am 
> interested to work for developing docking part of the code. Can any one 
> of the Gromacs administrators eloberate the plan to me and clarify me 
> the following points:
> 
> 1. If you already have a plan for docking implimentation, what type of 
> docking protocol was planned? (i.e., using algorithms like GA, etc. to 
> sample the space or other methods like fragment growth method)
GA works fine in Autodock. There are other methods of course.
> 
> 2. Will it be like combining both MD and docking? (i.e., like 
> constrained MD to simulate the drug free receptor and the drug binding 
> induced conformational changes of the side chains, etc).

This is up to you!

The main advantage of using GROMACS is speed, and the ability to use 
multiple force fields.

For rigid docking you could use the PME grid for evaluating long range 
Coulomb interactions (and you only have to build the grid once for the 
target protein). Short-range Coulomb / Van der Waals inteactions can be 
done with a cut-off.
> 
> I havent used CVS before. But I can learn it first and with the help of 
> all current developers, I think I can progress in this area.
>
This is described on the wiki as well.

> Thanks.
> 
> Sincerely,
> 
> ArunKumar. S
> 
> 
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-- 
David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se