[gmx-users] Docking

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 27 11:18:08 CEST 2011

On 4/27/2011 7:05 PM, mohsen ramezanpour wrote:
> Dear Users
> I read so many emails to mailing list, there were important notes 
> about docking but I couldn't extract a general result.
> Please let me know:
> 1-Can we dock a ligand to it's protein's binding pocket with Pymol and 
> Gromacs as following?
> first:locating ligand outside and close to binding site  manually in 
> pymol and saving complex.pdb
> second:doing all steps for generating complex.top and complex.gro as 
> Enzyme-Drug tutorial
> third:running md (with out any pull code and constraint),in the other 
> words,full flexible system.
> I think drug can move freely and according to it's interaction with 
> binding site can be attracted by binding site.
> reside for a distance time and then will come out of pocket.
> Am I right?

In principle, yes, but it is wildly unlikely that you have a system that 
can bind and unbind reliably in the 100ns simulation range that you 
might be able to afford to run, and if you did happen to have one, what 
would you have learned?

> I know what discussed in mainling list about deffinition of "Docking".
> 2-I have some docked files by "Docking Server " for some of my 
> drug-protein's complexes.
> now,I want to obtain them by doing MD in the above proccess.if I was 
> successful then try to do that for other drugs which I don't have any 
> docked pdb for them.
> How can I fit a trajectory with a typical pdb file?

I don't understand what you are asking.


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