Dear All, I need to add 6 CL ions to make the system neutral but when I type the command line genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6 and choose group 15 (SOL), the error is Fatal error: No line with moleculetype 'SOL' found the [ molecules ] section of file ‘topol.top’
when I check the ‘topol.top’ file I found there are 24504 SOL molecules present. My topology file looks like this ; Include water topology #include "amber99sb.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "amber99sb.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Ligand 1 SOL 24504 Please let me know how to rectify the problem regards, Ashima -- View this message in context: http://gromacs.5086.n6.nabble.com/genion-error-No-line-with-moleculetype-SOL-found-the-molecules-section-of-file-topol-top-tp5005363.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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
