can a system containing one protein and two different ligands been simulated by software gromacs?
i use two different ligands, that is, one is heme, the other graphene.
how to design this system.
I known the protein pdb file, and heme has been constructed by 54a7 force field， and graphene has been established by n2t program and used by oplsaa force field.
How can I fulfill the next work?
thank you very much.
You should not try to combine different force fields in a single system. Either generate everything under GROMOS96 54A7 or everything under OPLS-AA. Mixing force fields is unlikely to be a valid physical model.
You can combine any number of species into a single system. Just #include the appropriate .itp files, one for the ligand, and one for the graphene sheet.
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