[gmx-users] Docking

mohsen ramezanpour ramezanpour.mohsen at gmail.com
Wed Apr 27 11:52:20 CEST 2011

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?

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

On Wed, Apr 27, 2011 at 1:48 PM, Mark Abraham <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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