Hi, When I start from a energy minimized protein in vacuum and solvate it using genbox, the output message says that the protein has zero charge. So I skip the genion step. I follow this with energy minimization of the solvated protein followed by restraining the protein and then doing a short mdrun (as is the usual procedure outlined in most tutorials). However, when I run the grompp command as the first step for the position restrained md, it runs but prints a note saying that the system has non-zero charge ~ - 0.9999.
NOTE 2 [file finalnoss.top, line 8070]: System has non-zero total charge: -9.999994e-01 I dont understand. Do I need to run the genion step anyway or is it okay to continue with this system? Pooja -- Quaerendo Invenietis-Seek and you shall discover. -- Quaerendo Invenietis-Seek and you shall discover.
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