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Hello, All
I have prepared my protein topology using the AMBER 94 force field and TIP3P water model. I need to prepare ligand topology. I am facing difficulties during ligand topology file preparation. I used Acype online server (Acpype Server). I obtained one folder which has multiple files.
I want to perform the Build the Complex step now. For that I need .ini file. There are two prm, itp files in that folder like ligand_GMX_OPLS.itp, ligand_GMX.itp. There is no ini file for ligand also, but gro file is there for ligand.
Which parameter file (prm), topology (itp) should I consider for further analysis?