Hi Cristina, Previous ultra-long conventional molecular dynamics works have shown that ligand can find its binding pocket and finally bind in a crystal complex pose. Also enhance sampling techniques, e.g. metadynamics, can speeed the binding process.
So, if you want ligand to find its binding pocket, you may need long-time simulation or enhance sampling. Distance restraint on the ligand is harmonic force, it indeed can affect the interaction between ligand and protein. > -----原始邮件----- > 发件人: "Gonzalez Fernandez, Cristina" <cristina.gonzalezf...@unican.es> > 发送时间: 2020-03-20 17:59:05 (星期五) > 收件人: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org> > 抄送: > 主题: [gmx-users] Problem in protein ligand interaction > > Dear Gromacs users, > > > I'm trying to simulate a protein-lipid interaction. Analyzing the simulation, > it seems that the lipid does't have enough driving force to reach the binding > pocket, since van der Waals forces move the lipind towards the binding pocket > whereas electrostatics move the lipid in the opposite direction. How could I > achieve that the lipid reaches the protein binding site? Could I include some > distance restraints that help the lipid to move to the binding pocket and > then switch them off or this idea would lead to unreliabe results? > > > Thank you in advance for all your help! > > > Regards, > > > Cristina > -- > 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. -- Du, Yu PhD Student, Shanghai Institute of Organic Chemistry 345 Ling Ling Rd., Shanghai, China. Zip: 200032, Tel: (86) 021 5492 5275 -- 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.
