Deepak: Ag-Ab interactions occur via the hypervariable regions of the Ab. So the target amino acids for interaction will be much smaller. There are ample of docking softwares that can do this but that is a tricky affair at times. You may also look at protein-protein interaction softwares too.
Best RPS On Feb 23, 2018 9:45 PM, Krzysztof Makuch <krzysztof.mak...@gmail.com<mailto:krzysztof.mak...@gmail.com>> wrote: Hi, If you don't know where exactly binding occurs you can't really do this using only gromacs. I'd even suggest that until you have to, for antibodies it might be better to stick mostly to docking software. 1 - you have to have antibody and antigen parametrized using the same forcefield (FF). 2 - check stability in selected FF. Some make proteins more stable, other less. It is important to pay attention if your protein really have to be stable - for example if you take only part of the antibody it may not be stable either under physiological or in silico conditions. That's why you may have to use some restrains. Or you may not, you have to decide. 3 - you have to dock antigen in antibody using docking software (there are many...). Above 50% of results will be ridiculous, often the best energy still means stupid docking result. In many cases you may stop here, just use multiple docking engines, compare and you have supplementary materials for your molecular biology paper. If you are really stubborn and you have ligand parametrized: 4 - restrain both molecules, equilibrate 5 - turn off restrains and check if your complex is stable. For antibodies there is quite big chance that it won't be because: - Ab. is dynamic structure which may change shape after binding and docking can't simulate this - Water competes for H-bonds and nobody can guarantee that your complex is stable enough - you may have wrong var region. - the position of antigen may be slightly wrong and in result - break off 7. If everything is ok you can begin energy analysis - umbrella, FEP In general I advice against being stubborn until this is your primary project. Antibodies are nasty, little guys. Best, KM 2018-02-23 15<tel:2018022315>:24 GMT+01:00 Deep kumar <deepak.choube...@gmail.com<mailto:deepak.choube...@gmail.com>>: > Hi Gromacs users, > > I am studying antigen-antibody interaction at protein level. I have a > protein sequence (no crystal structure, length 180 residues) of the > antigen, and have predicted the secondary structure of it (and modeled). By > performing conserved domain search using inferno and NCBI I found out a > domain in the antigen - PCC1 (residue 90 to 160). I am interested to know > how the antigen interacts with the antibody (2000 residues) *in silico*. > The ultimate aim is to find out "how the antigen interacts with the > antibody, and predict the possible domains used by the antigen to interact > with the antibody". I would really appreciate your valuable suggestions on > how this can be done using GROMACS MD. Please let me know if I need to > provide any further information. Thanks for your time. > > Regards, > DK > -- > Gromacs Users mailing list > > * Please search the archive at <http://www.gromacs.org/> > http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read <http://www.gromacs.org/Support/Mailing_Lists> > http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to > gmx-users-requ...@gromacs.org<mailto:gmx-users-requ...@gromacs.org>. > -- Jagiellonian University Department of Computational Biophysics and Bioinformatics tel.1: (12) 664 61 49 tel.2: (48) 664 086 049 -- Gromacs Users mailing list * Please search the archive at <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read <http://www.gromacs.org/Support/Mailing_Lists> http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users>https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org<mailto: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.