[gmx-users] ions error
Hi all, After a ran grompp_d in prepration for a Steepest Descente Minimizations with constraints i got the folowing error message: Fatal error: No such moleculetype CL- I don know for shure but i think that i forgot to modify some of the files with the numbers os CL- ions I've introduced into the system. Here is the command line: grommp_d -f stpr.mdp -c sistema_ions.gro -p sistema.top -o sistema_stpr.tpr Thanks in advance. -- gmx-users mailing listgmx-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
Re: [gmx-users] ions error
Eduardo Oliveira wrote: Hi all, After a ran grompp_d in prepration for a Steepest Descente Minimizations with constraints i got the folowing error message: Fatal error: No such moleculetype CL- I don know for shure but i think that i forgot to modify some of the files with the numbers os CL- ions I've introduced into the system. No, the error is complaining about the ion name, not the number. If the numbering mismatched, you'd get something different. Check ions.itp for proper naming for your force field. Here is the command line: grommp_d -f stpr.mdp -c sistema_ions.gro -p sistema.top -o sistema_stpr.tpr The more relevant information would have been your genion command, force field name, and Gromacs version. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
Re: [gmx-users] ions error
Eduardo Oliveira wrote: OK, thanks for the info. I'm running GROMACS 4.5.5 Here is my genion command: genion_d -s sistema_stpr.tpr -o sistema_ion.gro -nname CL- -nn 3 -nq -1 -p sistema.top I chose the GROMOS force filed. Refer to the second paragraph of genion -h. -Justin *De:* Justin A. Lemkul jalem...@vt.edu *Para:* Eduardo Oliveira eduardo...@yahoo.com.br; Discussion list for GROMACS users gmx-users@gromacs.org *Enviadas:* Segunda-feira, 2 de Abril de 2012 16:55 *Assunto:* Re: [gmx-users] ions error Eduardo Oliveira wrote: Hi all, After a ran grompp_d in prepration for a Steepest Descente Minimizations with constraints i got the folowing error message: Fatal error: No such moleculetype CL- I don know for shure but i think that i forgot to modify some of the files with the numbers os CL- ions I've introduced into the system. No, the error is complaining about the ion name, not the number. If the numbering mismatched, you'd get something different. Check ions.itp for proper naming for your force field. Here is the command line: grommp_d -f stpr.mdp -c sistema_ions.gro -p sistema.top -o sistema_stpr.tpr The more relevant information would have been your genion command, force field name, and Gromacs version. -Justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- Justin A. Lemkul Ph.D. Candidate ICTAS Doctoral Scholar MILES-IGERT Trainee Department of Biochemistry Virginia Tech Blacksburg, VA jalemkul[at]vt.edu | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin -- gmx-users mailing listgmx-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
