Combining protein and ligand

User discussions
1

GROMACS version:5.1.4
GROMACS modification: Yes/No
Hi all,
How should I combine the receptor and ligands topology generated using charmmgui input generator and cgenff respectively to be used for gromacs MD run?
can they be combined before solvation and equilibration of the system (protein)

thanks for your answer

2

If you want CHARMM-GUI to build the system, upload the receptor-ligand complex coordinates and the server will call CGenFF to generate the ligand topology. The complex will then be solvated, etc. in subsequent steps. If you have questions about CHARMM-GUI, contact their developers directly.