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 <[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 > > > > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >
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