Alex, There are so many important reactions / applications in which protein polymer interactions play a role that the ability to generate of polymers should be part of gromacs repertoire. I’ll keep plugging away on this and report to the community if I can break the code - other than using the very good but terribly expensive commercial programs. I would not doubt that many have already accomplished this this task, but it is not well tracked within this group.
I might not approach a Molysulfidnitride substrate , ( making turbine blades ??) but TiO2 is indeed another surface very popular with proteins. Most every nitinol surface is essentially TiO2. If you have some pointers on that, I’m listening. Thank you again for the assist. Regards Paul > On Sep 27, 2018, at 3:16 PM, Alex <nedoma...@gmail.com> wrote: > > Hi Paul, > > Glad x2top is working out for you. The rest of the things you're pointing > out, I hope others could comment. I haven't simulated any proteins in a long > time, but if you ever need to drop a protein on the surface of some sort of > an insane molybdenum disulfide-graphene-boron nitride heterostructure, I > could be of service. ;) > > Alex > > > On 9/27/2018 10:44 AM, pbuscemi wrote: >> Alex, >> This pertains the prior correspondence to building a polymer and is the >> process I've been developing. >> >> To date I can obtain an ITP and pdb from ATB for a monomer. From there >> with information in those files, it is relatively easy to construct the n2t >> file to use in x2top. ( I’d be happy to provide an example as a 'tutorial' >> of sorts). X2top provides the monomer rtp for use in pdb2gmx. It has all >> the atom type information. Thanks for the guidance on that. >> >> The hangups are not associated with the rtp but of all things producing the >> pdb of the polymer specifically positioning along,say, the x axis but more >> importantly, producing the pdb of the polymer that uses the same atom labels >> as the original pdb of the monomer. In the PE example from gromacs there >> are 3 mers of 2 atoms so it is easy to manually keep track of the names, >> but not if you have 1000 mers. Avogadro renames the added mers. >> >> Since gromacs can build proteins, and I can tell gmx that the monomer is a >> protein ( it wants to think that it is anyway), I will try to use the same >> logic to build the polymer. More to come. >> >> Paul >> >> >> > > -- > 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.
