[gmx-users] Docking

Mark Abraham Mark.Abraham at anu.edu.au
Wed Apr 27 12:27:15 CEST 2011

On 4/27/2011 7:52 PM, mohsen ramezanpour wrote:
> Dear Mark
> Thank you for your reply.yes,you are right.
> Regarding question 2:
> I have a pdf file from "Docking Server" for sertraline-SERT 
> example.Suppose this is a good docked state.
> In the other hand,I did what I explained in section 1 for sertraline 
> and SERT.(by pymol and ...)
> Now, I want to check if I have docked sertraline to SERT correctly or 
> not( by comparing with Docking server's one)
> How can I do that?

Comparing MD-docked structures and otherwise-docked structures is easy - 
look at the RMS deviation of atom positions, to start with. However, a 
small or large deviation is not evidence that either docked structure 
bears any relationship to what happens in vivo.

> Do you have any suggestion for doing docking by gromacs? for example 
> pulling code, MD , or SMD?

People use these kinds of methods for good reasons. Time spent reading 
up on how and why is time well spent.


> Thanks in advance
> On Wed, Apr 27, 2011 at 1:48 PM, Mark Abraham <Mark.Abraham at anu.edu.au 
> <mailto:Mark.Abraham at anu.edu.au>> wrote:
>     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.
>     Mark
>     -- 
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