On 12/9/14 9:25 AM, Hassan Aaryapour wrote:
Dear Gromacs Users, I'm new in gromacs and I have been trying to add ions to the simulation box using following command in gromacs 5: gmx genion -s ions.tpr -o conf-ion.pdb -p topol.top -neutral -conc 0.15 then I selected these groups(Protein, MG, Ligand, respectively): 1 | 13 | 14 This error was appeared: Program gmx, VERSION 5.0 Source code file: /home/QMMM/ProgramFiles/gromacs-5.0/src/gromacs/gmxana/gmx_genion.c, line: 503 Fatal error: Your solvent group size (2701) is not a multiple of 9 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors I found this URL " http://comments.gmane.org/gmane.science.biology.gromacs.user/64577"; in related to my question but i don't understand answer to resolve my error? Indeed, I 've already successfully simulated another protein with same gromacs and commands.
You shouldn't be replacing a merged group of protein, Mg, and ligand with ions. You need to choose some sort of solvent (water) with ions. This requires no custom group to do.
-Justin -- ================================================== Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 629 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul ================================================== -- 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.
