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.
Mark
Thanks in advance
On Wed, Apr 27, 2011 at 1:48 PM, Mark Abraham <[email protected]
<mailto:[email protected]>> 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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