Re: [gmx-users] Index error
Please don't reply to the whole digest. On 7/25/13 1:47 PM, Collins Nganou wrote: Dear Justin, Thanks for your answer... I move so far... My aim was to ask gromacs to read directly a modify protein SOL+NA, not protein SOL NA But I have not succeed so far. I don't understand what you're asking here, and without exact commands, output, .mdp settings, etc there's little anyone can do to assist you. Again, the task that you need to carry out is described explicitly in most tutorials so please do make an effort to follow existing protocols. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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] Index error
Dear Users, I would like to know if anyone may help me understand how to update the index file. I am trying to simulate a dna in solution. I have relaxed a Solvent with attached min.mdp file without problem. in the second step I was intended to relax SOL + Na DNA with 20ps.mdp. But the index file did not work. I have trying to generate an index file using the file.gro from min.mdp but it doesn't work. Below is the obtained error. Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'DNA_chain_B' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning H bonds into constraints... Velocities were taken from a Maxwell distribution at 10 K --- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line: 1332 Fatal error: Group NA+SOL referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or custom index group names, in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- I am looking forward to have any suggestion that might help me in this case. I wish all of you a wonderful day. Collins -- 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] Index error
On 7/24/13 8:34 AM, Collins Nganou wrote: Dear Users, I would like to know if anyone may help me understand how to update the index file. I am trying to simulate a dna in solution. I have relaxed a Solvent with attached min.mdp file without problem. in the second step I was intended to relax SOL + Na DNA with 20ps.mdp. But the index file did not work. I have trying to generate an index file using the file.gro from min.mdp but it doesn't work. It is simple to merge solvent and ion groups. See tutorial material or type 'help' at the make_ndx prompt. We can't help you if we don't know what you did. Below is the obtained error. Generated 2211 of the 2211 non-bonded parameter combinations Generating 1-4 interactions: fudge = 0.5 Generated 2211 of the 2211 1-4 parameter combinations Excluding 3 bonded neighbours molecule type 'DNA_chain_B' turning H bonds into constraints... Excluding 2 bonded neighbours molecule type 'SOL' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'NA' turning H bonds into constraints... Excluding 1 bonded neighbours molecule type 'CL' turning H bonds into constraints... Velocities were taken from a Maxwell distribution at 10 K --- Program grompp, VERSION 4.5.5 Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line: 1332 Fatal error: Group NA+SOL referenced in the .mdp file was not found in the index file. Group names must match either [moleculetype] names or custom index group names, in which case you must supply an index file to the '-n' option of grompp. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- If you use make_ndx, group names will never contain + signs. Merged groups are joined via _ (underscore), but it sounds like you haven't even gotten that far, given the statement above. -Justin -- == Justin A. Lemkul, Ph.D. Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 == -- 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
