GROMACS version:
GROMACS modification: Yes/No
I would like to consult about performing a combined-force field simulation using GROMACS. Below is my approach (though I am unsure if it is entirely correct): I intend to use the GLYCAM force field for the oligosaccharide ligand and the AMBERff99SB force field for the glycosidase. I generated the oligosaccharide file using the CHARMM-GUI website, performed molecular docking with AutoDock Vina, then extracted the protein and oligosaccharide. I generated my oligosaccharide-TIP3P file via GLYCAM-Web, and subsequently used AmberTools to replace the coordinates of the docked oligosaccharide with those of the oligosaccharide generated from GLYCAM-Web, converting them into GRO and TOP files while modifying the small molecule files. However, when merging the protein-ligand files for simulation, a warning about duplicate atom definitions first appears. After ignoring this warning, during the NVT equilibration step, LINCS warnings arise, preventing further progress. Therefore, I would like to ask how I should revise my approach and steps to complete the combined-force field simulation. Thank you very much!
