[gmx-users] force field not found
nedomacho at gmail.com
Sun Sep 30 07:43:30 CEST 2018
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
On 9/29/2018 8:58 PM, paul buscemi wrote:
> 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.
>> On Thu, Sep 27, 2018 at 4:11 PM paul buscemi <pbuscemi at q.com> wrote:
>>> 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.
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