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On 4/27/2011 7:52 PM, mohsen ramezanpour wrote:
<blockquote
cite="mid:BANLkTikK78dY35r97bniGoysWzVd4cuzbQ@mail.gmail.com"
type="cite">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>
</blockquote>
<br>
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.<br>
<br>
<blockquote
cite="mid:BANLkTikK78dY35r97bniGoysWzVd4cuzbQ@mail.gmail.com"
type="cite"><br>
Do you have any suggestion for doing docking by gromacs? for
example pulling code, MD , or SMD?<br>
</blockquote>
<br>
People use these kinds of methods for good reasons. Time spent
reading up on how and why is time well spent.<br>
<br>
Mark<br>
<br>
<blockquote
cite="mid:BANLkTikK78dY35r97bniGoysWzVd4cuzbQ@mail.gmail.com"
type="cite">
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 moz-do-not-send="true"
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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</font></blockquote>
</div>
<br>
</blockquote>
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