Dear Mark<br>Thank you for your reply.yes,you are right.<br><br>Regarding question 2:<br>I have a pdf file from "Docking Server" for sertraline-SERT example.Suppose this is a good docked state.<br><br>In the other hand,I did what I explained in section 1 for sertraline and SERT.(by pymol and ...)<br>
Now, I want to check if I have docked sertraline to SERT correctly or not( by comparing with Docking server's one)<br>How can I do that?<br><br><br>Do you have any suggestion for doing docking by gromacs? for example pulling code, MD , or SMD?<br>
Thanks in advance<br><br><br><div class="gmail_quote">On Wed, Apr 27, 2011 at 1:48 PM, Mark Abraham <span dir="ltr"><<a href="mailto:Mark.Abraham@anu.edu.au">Mark.Abraham@anu.edu.au</a>></span> wrote:<br><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im">On 4/27/2011 7:05 PM, mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear Users<br>
<br>
I read so many emails to mailing list, there were important notes about docking but I couldn't extract a general result.<br>
Please let me know:<br>
<br>
1-Can we dock a ligand to it's protein's binding pocket with Pymol and Gromacs as following?<br>
<br>
first:locating ligand outside and close to binding site manually in pymol and saving complex.pdb<br>
second:doing all steps for generating complex.top and complex.gro as Enzyme-Drug tutorial<br>
third:running md (with out any pull code and constraint),in the other words,full flexible system.<br>
<br>
I think drug can move freely and according to it's interaction with binding site can be attracted by binding site.<br>
reside for a distance time and then will come out of pocket.<br>
<br>
Am I right?<br>
</blockquote>
<br></div>
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?<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
I know what discussed in mainling list about deffinition of "Docking".<br>
<br>
<br>
2-I have some docked files by "Docking Server " for some of my drug-protein's complexes.<br>
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.<br>
<br>
How can I fit a trajectory with a typical pdb file?<br>
</blockquote>
<br></div>
I don't understand what you are asking.<br>
<br>
Mark<br><font color="#888888">
<br>
<br>
<br>
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