[gmx-users] double bond

[Ehsan Sadeghi]

Hi gromacs users,

In my nafion sidechain, I have -CF2-SO3H. In this molecule, S atom has 2 double bonds with 2 O, 1 single bond with another O, and i single bond with C (total 6 bonds). When I do energy minimization in vacuum, I got two F atoms nonbonded to my C atom. I think, gromacs generate triple bonds between C and S and 3 single bonds between S and 3 O atoms.

I added these commands in specbond.dat to resolve the issue

NAF     S       6       NAF     O4      2       0.3     NAF     NAF
NAF     S       6       NAF     O5      2       0.3     NAF     NAF

But, it didn't solve my problem.

Any suggestion for solving this problem? 

Regards,
Ehsan