Re: [gmx-users] reg grompp error in QM/MM of mopac gromacs
- Original Message - From: vidhya sankar scvsankar_...@yahoo.com Date: Wednesday, September 15, 2010 16:22 Subject: [gmx-users] reg grompp error in QM/MM of mopac gromacs To: gmx-users@gromacs.org --- | Dear sir/Madam thanks in Advance i wanted to do QM/MM for simple peptide .i have edited my topology files as given in the manual i also include the Link atom(LA) under [DUMMIES2] secction of my topology .but when i run the following grompp command ./grompp_d -f em.mdp -c spep_b4em.gro -p spep.top -o spep_em.tpr I got the error as follows Back Off! I just backed up mdout.mdp to ./#mdout.mdp.29# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp --- Program grompp_d, VERSION 4.0.7 Source code file: topdirs.c, line: 99 Fatal error: Invalid pairs type 0 --- the suggestions are highly appericiated Something's wrong with your topology. We can't guess what based on this information. Reread the instructions and check that your modifications to your .top comply. Mark | --- -- 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] reg grompp error in QM/MM of mopac gromacs
On 2010-09-15 07.55, vidhya sankar wrote: Dear sir/Madam thanks in Advance i wanted to do QM/MM for simple peptide .i have edited my topology files as given in the manual i also include the Link atom(LA) under [DUMMIES2] secction of my topology .but when i run the following grompp command ./grompp_d -f em.mdp -c spep_b4em.gro -p spep.top -o spep_em.tpr I got the error as follows Back Off! I just backed up mdout.mdp to ./#mdout.mdp.29# checking input for internal consistency... processing topology... Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6.itp Opening library file /usr/local/gromacs/share/gromacs/top/ffG53a6nb.itp the instructions are outdated. [ dummies2 ] should be replaced by [ virtual_sites2 ] (check the manual for exact syntax). --- Program grompp_d, VERSION 4.0.7 Source code file: topdirs.c, line: 99 Fatal error: Invalid pairs type 0 --- the suggestions are highly appericiated -- David van der Spoel, Ph.D., Professor of Biology Dept. of Cell Molec. Biol., Uppsala University. Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se -- 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
