Hi Mark, I want to refine the model for any bad contact if the structure has. This article support the simulation of any homology model after its creation by homology modeling approach " https://www.ncbi.nlm.nih.gov/pubmed/22513870?dopt=Abstract". Do you please think that there is no need to refine the model via simulation? or the claim which i do for refinement via simulation, is biased?
Thanks for consideration! Amir On Wed, Dec 21, 2016 at 10:09 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > What us the purpose in doing MD on the homology model? That'll tell you > whether you need a model with the other parts. > > Mark > > On Thu, 22 Dec 2016 16:51 Amir Zeb <zebami...@gmail.com> wrote: > > > Hello, > > > > I have created a homology model for a protein, where the seq. identity > > between the template and target is 40%. The template structure also > > contains co-factor and an inhibitor in bound form means it is a complex. > > I'll have to define the ligand binding site in target (homology model) > > based on inhibitor bound in template structure. But before to reach that > > stage, i want to simulate the created model to refine the structure which > > is a common practice in modelling. I'm not pretty sure that should i > > simulate the model structure along with the inhibitor and co-factor from > > template, or one of them, or just only the protein structure alone? > Please > > let me, if you have any referenced answer. > > > > Regards > > > > Amir > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.