On Thu, Jan 25, 2018 at 7:43 PM, alex rayevsky <rayevsk...@gmail.com> wrote:
> Dear users and developers! > > I have a question about replica exchange sampling and simulation annealing > method. Well, I have a protein (TubulinG) X-ray, however it lack last 10-11 > residues, which are probably exposured to the solvent (and it seems are > flexible enough to be invisible for X-ray). The protein exists in two > isoforms, which differ on a single amino acid (approximately -15 position > from the end), however, some in-house biochemical experiments stated that > this change is crucial for motility of these terminal 10-15 residue. > > The problem is that I can't predict the exact initial location/conformation > of the full-length C-termini and all standard MD simulations showed > different, not similar, positions of the region - it can be either flexible > or pinned to the 'protein's body' during the MD. It seems, that it depends > on the seed which turns on a trigger for rotation of exposured straight > 10-15 res. C-termini... Before starting a production MD for subsequent > analysis I should be somehow ensured that the initial conformation is > reliable. i-Tasser is not a good way, because it doesn't guarantee nothing, > except the total minimization state, and homology modelling is also > impotent. > Hi.. all the best. Start with errors is what I personally advice. Rosetta fragment assembly method is one good approach or try contact approach method. I believe they are good in defining protein structure. Thank you > > That is why I want to start a preliminary MD to sample these C-terminal end > (rebuild with any program like pymol, molsoft or swissmodel server) and I > bet on these two approaches, mentioned above. > > Does anybody know is it possible, reasonable? > where I can find a working tutorial to provide some changes or use it as it > is? > The additional question is about 'partial application' of the method to the > fragment of the protein, to avoid time consuming calculations for the whole > system, which is not a priority, as the final goal is just a minimized > protein with a more informed preparation alghorithm. > > Thank You in advance!!! > > > > *Nemo me impune lacessit* > -- > 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. > -- *Regards,* *Rahul Suresh* *Research Scholar* *Bharathiar University* *Coimbatore* -- 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.