[gmx-users] Adding a Mg2+ Dummy model to GROMACS AMBERff03
olaf2745 at yahoo.de
Mon Oct 9 21:24:02 CEST 2017
I am adding a Mg2+ Dummy model to the AMBERff03 FF in GROMACS 2016.3,using the paramters from Jiang et al. (given in the supporting material)
http://pubs.acs.org/doi/abs/10.1021/acs.jcim.5b00286as the newest and "most reliable for ATP-Mg2+-Protein conformations".
I was able to implement all parameters except Ai and Bi on page 5/16 in the supporting material.Vice versa i am missing the parameters "sigma" and "epsilon" for the dummy model in the ffnonbonded.itp file of the FF.
I am not sure how to translate Ai and Bi to "sigma" and "epsilon" and I would be glad if someone could help.
If someone did this already I also would be thankful if I could get a record of all changes, you did, in the gromacs Amberff03 FF.
Thank you very much,Sincerly,olaf
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