Hi all, After running the following command <b>perl inflategro.pl system.gro 4 POPC 14 system_inflated.gro 5 area.dat</b> I modified the lipids in the topol.top file and in system.gro file the no of lipids and no of atoms respectively.
but after that for energy minimization when i ran the following command: <b>grompp -f EM.mdp -c system.gro -p topol.top -o em.tpr</b> It is showing the following error. Please tell me if the command is right or not and if it is right then what can be done to resolve and why exactly it is showing this error. I checked the topology file but i am not able to reach any conclusion. Please guide me as most of you have faced this error and got the solution for it . <b>Ignoring obsolete mdp entry 'title' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.2# Generated 867 of the 1891 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein' Excluding 3 bonded neighbours molecule type 'POPC' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 1 [file topol.top, line 21239]: System has non-zero total charge: 3.000002 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. ------------------------------------------------------- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/grompp.c, line: 523 Fatal error: number of coordinates in coordinate file (system.gro, 10019) does not match topology (topol.top, 17093) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors</b> Thanks in advance. -- 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
