Dear users, I get topology (A.itp) and structure (A.gro) files of a ligand using Automated Topology Builder. A.gro file has optimised geometry. That is, the coordinates of the atoms have been changed according to the initial file .pdb. I am confused. When I do simulation related to protein-ligand interactions, which coordinates I use? Optimised coordinates obtained from the Automated Topology Builder or original coordinates in .pdb?
Thanks in advance -- Ahmet Yıldırım -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * 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
