Hi. I've been trying to build my system in gromacs and have run into a problem. On my initial energy minimization after building the .go and .top files, I inevitably get 1 atom that doesn't get below the specified fmax (fmax of 10 in my case: the force on the atom is around 60-90). This remains true after multiple rounds of minimization using both steepest descent and CG algorithms. The atom in question is always a hydrogen at the D1 or E2 position in one of the histidines. I've tried both letting pdb2gmx assign the histidine protonation states and using proPKA to assign them and then making pdb2gmx use those assignments with the -his tag.
So far nothing has worked. Any suggestions?
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