On 1/27/14, 2:15 PM, José Adriano da Silva wrote:
I am new to Gromacs, then follow the tutorial protein-ligand, decided to adapt the procedure for my protein (acetylcholinesterase) and my binder. The procedure is this (protein-ligand complex): <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/comp lex/index.html> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/compl ex/index.html Well, I switched to facilitate the name of my protein and my binder by the names used in the tutorial. The problem occurs when I do the command: grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr The following error occurs: Fatal error: Molecule type 'Protein_chain_A' contains no atoms
The error suggests that the topology is probably empty, which you can inspect with a text editor. Maybe pdb2gmx failed, but the fatal error from that step should have been quite obvious. Otherwise, some modification that you have made to the topology has rendered its format unintelligible.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
