Hi all, I am trying to put a tetrameric protein for Energy Minimization to be followed by MD simulation of course. But, my problem is that it is a tetramer and also I need to perform the simulation with the ligand. I have read the tutorial for Protein-Ligand simulation but that explains for only one chain, whereas I am talking about 4 chains here. I need to put in my tetramer with ligands attached for simulations. If I have understood correctly, the tutorial mentions about extracting the ligand from PDB and then copying the PDB file of the extracted ligand into PRODRG and then retrieving the topology file from there and appending it to the topology output of the protein without ligands attached. But this is specific for one chain i.e. the PDB co-ordinate given to PRODRG is for the ligand from one chain. The second question is that can I not submit the whole protein-ligand complex to GROMACS and then run pdb2gmx for generating topology. How do I go about that? I understand that I would have to change the top directories of GROMACS to accommodate my ligands but I don't know how to do that.
I know my question might be really silly but I am short of time at the moment and would really appreciate any help in this matter. Best Wishes, -- Ankita Naithani -- Ankita Naithani -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists