[gmx-users] force field not found

paul buscemi pbuscemi at q.com
Sun Sep 30 04:58:12 CEST 2018


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.


> On Sep 27, 2018, at 5:47 PM, Alex <nedomacho at 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 <pbuscemi at 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-request at gromacs.org.

More information about the gromacs.org_gmx-users mailing list