[gmx-users] force field not found

[paul buscemi]

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 <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
>> 
>> 
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