Alex, Justin, I've managed to make and run polymers using Avogadro ,modifying the n2t, then creating the top using x2top under 54a7 ff. The method may be useful for others but before presenting it to the user group, it should be reviewed so that glaring mistakes/concepts are revised. If you think it worthwhile, would either of you be agreeable to reviewing the process?
Thanks Paul -----Original Message----- From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se [mailto:gromacs.org_gmx-users-boun...@maillist.sys.kth.se] On Behalf Of Alex Sent: Sunday, September 30, 2018 12:44 AM To: gmx-us...@gromacs.org Subject: Re: [gmx-users] force field not found Yeah, if it is missing bonded parameters, you can always try to find something similar, at least with OPLS-AA -- don't really know about the other ff. Alex On 9/29/2018 8:58 PM, paul buscemi wrote: > 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. -- 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.
