I am looking for a forcefield in GROMACS which better characterizes the TCDD ligand.
In particular I have found that OPLS-AAx seems suitable [J Chem Theory Comput. 2012 Oct 9;8(10):3895-3801].
Unfortunately, the authors told me to contact the GROMACS community for the specific implementation.
Do you know something about it? Could you suggest alternatives for halogen bonding treatment?
I don't know about GROMACS, but check this paper, it may be helpful for you
[1] M.A.A. Ibrahim, AMBER empirical potential describes the geometry and energy of noncovalent halogen interactions better than advanced semiempirical quantum mechanical method PM6-DH2X., J. Phys. Chem. B. 116 (2012) 3659–69.
I hope it helps somehow.
Regards
I use halogen-bonding modification of GAFF in gromacs:
http://dx.doi.org/10.1021/ct2008389
You don't need to do any coding, but to set-up the topology may be a bit tricky. Write me a personal message if you need some help.
Is your problem with bonded interactions or non-bonded ones? if it is bonded interactions, just define a new atom type and bond interaction accordingly in the current force field you are using. If your problem is with vdW parameters, there are nothing much that you can do, as you may need to re-optimize the whole force field. If you have problem with partial charges, just calculate them with an appropriate method and add them to your aminoacid.rtp file in force field you are using in gromacs.
- Badges
- Science topic
- Similar topics
- Chemistry
- Theoretical Chemistry
- Computational Chemistry
- Molecular Dynamics