Dear Aldo Thank you for your reply Mark's notes and yours were very useful.
Best mohsen On Wed, Apr 27, 2011 at 6:46 PM, Aldo Segura <[email protected]>wrote: > Before making a MD simulation you should try to explore different ways to > analyze your docking results. For example, performing the same experiment > with different docking programs and scoring functions (“consensus scoring”) > and compare the results, is there consistency between them?. Now, if docking > results are not successful in terms of prior knowledge of your system (is > there structural information of your system? articles?), you could select > several of the complex predicted by the docking program and make a MD > simulation and free energy calculation, compare the results for each complex > and verify if the results improve according to what you expected. However, > as mentioned by Mark, simulations and calculations like these involve much > computational resources and time. > > > > Best regards, > > > Aldo > > ** > > *======================================= > Aldo Segura-Cabrera > Laboratorio de Bioinformática > Centro de Biotecnología Genómica > Instituto Politécnico Nacional > Blvd. Del Maestro esquina Elías Piña, 88710 > Reynosa, Tamaulipas, México. > (899)9243627 ext. 87747 > e-mail: [email protected]; [email protected] > =========================================* > > > --- El *mié 27-abr-11, Mark Abraham <[email protected]>* escribió: > > > De: Mark Abraham <[email protected]> > Asunto: Re: [gmx-users] Docking > A: "Discussion list for GROMACS users" <[email protected]> > Fecha: miércoles, 27 de abril de 2011, 5:27 > > 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]<http://mc/[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://mc/[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]<http://mc/[email protected]> > . > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -----Sigue archivo adjunto----- > > -- > gmx-users mailing list > [email protected]<http://mc/[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]<http://mc/[email protected]> > . > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > -- > 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? 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