Re: [gmx-users] Re: g_hydorder
First I created index file with all oxygen atoms of water molecules using make_ndx -f lys_full.gro -o index_soloxy.ndx Then I used g_hydorder -f lys_full.xtc -s lys_full.tpr -n index_soloxy.ndx -or file1.out file2.out Following output appeared: Program g_hydorder, VERSION 4.6.3 Source code file: /root/gromacs-4.6.3/src/tools/gmx_hydorder.c, line: 702 Fatal error: No or not correct number (2) of output-files: 1 For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors Please guide me in filing redmine issue. I have read following link: http://www.gromacs.org/Developer_Zone/Redmine But could not locate link to file redine issue. On Wed, Oct 2, 2013 at 12:41 AM, David van der Spoel sp...@xray.bmc.uu.sewrote: On 2013-10-01 19:51, Nidhi Katyal wrote: Please provide me with necessary guidance. I have already posted this thrice but have not got a single reply Thanks in advance. On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal nidhikatyal1...@gmail.com* *wrote: Hello everyone, I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_2.out -n index.ndx I am getting following error; No or not correct number (2) of output files :1 Please give exact command line with file names and output cut-and pasted. The program needs indeed two output files of both types. It seems that your command line is ok nevertheless. Please file a redmine issue and assign it to me. It seems from above that correct number should be 2 but user is supplying only 1 and so is the error. But I am giving names of two output files. Also, I am unable to understand what exactly is contained in these two/four output files. I tried to comprehend this by looking at gmx_hydorder.c and could make a guess that I actually need sgmol/sgmean (variables as defined in program) as the final output. Please help me understand the usage of this command in order to fulfill my aim.I have posted this twice but have not got a single reply. Thanks in advance. -- 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-usershttp://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/** Support/Mailing_Lists/Searchhttp://www.gromacs.org/Support/Mailing_Lists/Searchbefore 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_Listshttp://www.gromacs.org/Support/Mailing_Lists -- 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] Re: g_hydorder
Please provide me with necessary guidance. I have already posted this thrice but have not got a single reply Thanks in advance. On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal nidhikatyal1...@gmail.comwrote: Hello everyone, I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_2.out -n index.ndx I am getting following error; No or not correct number (2) of output files :1 It seems from above that correct number should be 2 but user is supplying only 1 and so is the error. But I am giving names of two output files. Also, I am unable to understand what exactly is contained in these two/four output files. I tried to comprehend this by looking at gmx_hydorder.c and could make a guess that I actually need sgmol/sgmean (variables as defined in program) as the final output. Please help me understand the usage of this command in order to fulfill my aim.I have posted this twice but have not got a single reply. 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] Re: g_hydorder
On 2013-10-01 19:51, Nidhi Katyal wrote: Please provide me with necessary guidance. I have already posted this thrice but have not got a single reply Thanks in advance. On Tue, Oct 1, 2013 at 3:40 PM, Nidhi Katyal nidhikatyal1...@gmail.comwrote: Hello everyone, I would like to calculate angle tetrahedral order parameter of water molecules as defined by Chau et al (eq 3). I am using g_hydorder of gromacs 4.6.3 with my index group containing all oxygen atoms of water: g_hydorder -f *.xtc -s *.tpr -o file1.xpm file2.xpm -or file_1.out file_2.out -n index.ndx I am getting following error; No or not correct number (2) of output files :1 Please give exact command line with file names and output cut-and pasted. The program needs indeed two output files of both types. It seems that your command line is ok nevertheless. Please file a redmine issue and assign it to me. It seems from above that correct number should be 2 but user is supplying only 1 and so is the error. But I am giving names of two output files. Also, I am unable to understand what exactly is contained in these two/four output files. I tried to comprehend this by looking at gmx_hydorder.c and could make a guess that I actually need sgmol/sgmean (variables as defined in program) as the final output. Please help me understand the usage of this command in order to fulfill my aim.I have posted this twice but have not got a single reply. Thanks in advance. -- 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
