[gmx-users] Regarding error in ion neutralization step
Dear All Could any one help me to solve this error in gromacs 4.5.5 version. I am running dynamics on apo protein and the protein shows negative charge of -6 (after choosing OPLS-AA force filed) and when i was neutralizing the -6 with +6 and generating the genion.tpr file there it shows No such moleculetype NA+ error. But the same protein was running with out any error message in gromacs 4.0.7 version. The error message was given below. Kindly rectify the problem === [student@localhost gro]$ grompp -f em.mdp -p topol.top -c genion.gro -o genem.tpr Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype NA+ For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Regards Kirubakaran P -- 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
[gmx-users] Regarding error in ion neutralization step
Dear All Could any one help me to solve this error in gromacs 4.5.5 version. I am running dynamics on apo protein and the protein shows negative charge of -6 (after choosing OPLS-AA force filed) and when i was neutralizing the -6 with +6 and generating the genion.tpr file there it shows No such moleculetype NA+ error. But the same protein was running with out any error message in gromacs 4.0.7 version. The error message was given below. Kindly rectify the problem === [student@localhost gro]$ grompp -f em.mdp -p topol.top -c genion.gro -o genem.tpr Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype NA+ For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Regards Kirubakaran P -- 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] Regarding error in ion neutralization step
On 5/11/2011 1:05 AM, kirubakaran palani wrote: Dear All Could any one help me to solve this error in gromacs 4.5.5 version. I am running dynamics on apo protein and the protein shows negative charge of -6 (after choosing OPLS-AA force filed) and when i was neutralizing the -6 with +6 and generating the genion.tpr file there it shows No such moleculetype NA+ error. But the same protein was running with out any error message in gromacs 4.0.7 version. The naming convention has changed. See share/top/oplsa.ff/ions.itp Mark The error message was given below. Kindly rectify the problem === [student@localhost gro]$ grompp -f em.mdp -p topol.top -c genion.gro -o genem.tpr Ignoring obsolete mdp entry 'cpp' Back Off! I just backed up mdout.mdp to ./#mdout.mdp.3# Generated 332520 of the 332520 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 332520 of the 332520 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 2 bonded neighbours molecule type 'SOL' --- Program grompp, VERSION 4.5.5 Source code file: toppush.c, line: 1987 Fatal error: No such moleculetype NA+ For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- Regards Kirubakaran P -- 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
