Alex, I wanted to practice some more with x2top using a simple CH3 -( CH2)14 -Ch3 pdb model. oplsaa works fine, but not 54a7 FF generating the erro “ cannot find forcefield for C “ Th two CH3’s do not cause the error found but the fourteen CH2’s.
In the ffbonded.itp bond angle types i see CH2-S-CH3 , C-CH2-C and CH2-S_S, but not C-CH2-C. Can I add a new atomas ga 5_55 by anology or hunt for the correct parameters ? (I’ m trying his now ) I am assuming the n2t nor the rtp do not have to be modified since x2top does not rely on the rtp. This is a fairly basic but essential task, and would surly like to master it. Thanks, Paul > On Sep 27, 2018, at 5:47 PM, Alex <nedoma...@gmail.com> wrote: > > Never dealt with TiO2, but the path to parameterizing forcefields for > solid-state structures in MD is becoming more and more straightforward, > e.g., J. Phys. Chem. C 2017. 121(16): p. 9022-9031. > > Alex > > On Thu, Sep 27, 2018 at 4:11 PM paul buscemi <pbusc...@q.com> wrote: > >> 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 >> >> > -- > 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.
