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
> 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.
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