I posted my question in wrong forum, so here i am posting the same question aagin.
What is the parameter set to be used for GBSA for a system containing ATP in it?
The c30test/gbmv.inp recommends charmm19 parameter set, but it dosen't have ATP.
When I use charmm27 force field with stream file "toppar_all27_na_nad_ppi.str" i get total protein charge (+1) and upon adding ATP, protein+ATP charge becomes (-3). Adding Mg ions to neutralize ATP won't make any sense, until I use something like Lu(+3) ion.
What is the solution to the problem to make the total charge of the system neutral?