Hello GROMACS users,
I was trying to create an input file for energy minimization of solvated system, using the following command: grompp -v -f minim.mdp -c protein-solvated.gro -p protein.top -o protein-EM-solvated.tpr Got the following error: number of coordinates in coordinate file (1y6l-solvated.gro, 181577) does not match topology (1y6l.top, 182265). I think the following error occurred because I skipped the following step: Edit the topology file and decrease the number of solvent molecules. Also add a line specifying the number of NA ions and a line specifying the amount of CL. My question: 1. How to open the topology file? 2. How do I determine number of NA and CL ions added? I just saw a massive list of these counterions being added, but not the total number. 3. My net charge on the protein was 6+, why do I need to add Na+ ions? Any insight would be appreciated, Thank you, Neena Eappen Graduate Student Jockusch Lab<http://www.chem.utoronto.ca/wp/jockusch/>, U of T -- 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 [email protected].
