GROMACS version: 2024
Hello, is there any tutorial for simulating a protein-ligand-membrane system? I am familiar with simulating protein and protein-ligand. I know how to build a membrane system on CHARMM-GUI but never proceeded with the actual simulation. Should I prepare the membrane system using the protein-ligand complex pdb file? and for the simulation kindly let me know if there is any tutorial? Thanks.
Hi, I do not have a lot of experience but currently I am performing a MD simulation with membrane receptor and ligands.
Particulary, I prefered to prepare the membrane receptor entity with CHARMMGUI and develop the NVT equilibration step with CHARMMGUI too. After get the pre-nvt system in .pdb and the steps nvt.mdp configurations with constrains created (.itp files) by CHARMMGUI, I started to generate the pre-nvt system .gro file without waters using gmx pdb2gmx. In sequence, I applied the tutorial of Ligand-protein complex and the membrane protein tutorial, at this final tutorial only consider the steps after the membrane building. When I arrives in minimization steps in both equilibrations I used the information of the em.mdp, nvt.mdp and .itp generated by CHARMMGUI to adpt the simulation.
Hello Thank you for the response. It is however still not that clear. Would you mind sharing an email that I can contact you?
Yes, you can. my e-mail: daniel.g.ruiz@unesp.br