Hi Ghosh, Thanks for your answer. But I'm not sure if I understood what you meant. I already used insert-molecules command to create a box with the cationic species. Now, should I use the same command to include the anionic species into the box?
Best *Prof. Dr. Ednilsom OrestesDepartamento de Ciências Exatas - Sala C19Escola de Engenharia Industrial Metalúrgica de Volta Redonda* *Universidade Federal FluminenseR. dos Trabalhadores, 420 - Vila Santa Cecília* *Volta Redonda**, Rio de Janeiro, Brasil* *CEP 27255-125* *Tel: +55-24-2107-3777* 2017-09-05 17:24 GMT-03:00 soumadwip ghosh <soumadwipgh...@gmail.com>: > Hi, > > I am not sure why you used the gmx solvate command for putting the > anionic species in your simulation box. It is meant for filling up the > simulation box with water molceules as the resname 'SOL' in the > topol.top file. Thus when you hit grompp it expects 'SOL' entry in > your topology file, cant find it and prints an error. In my opinion, > one should use the same gmx insert-molecules command for inserting the > anionic part into the box. If you dont want to use water in the > simulation you can proceed without the solvation step but cant use gmx > solvate for inserting anionic species or anything else. > > Best > Soumadwip Ghosh > Post Doctoral Research Associate > City of Hope Cancer Research Center > Duarte 91010 CA > USA > -- > 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. > -- 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.