I'm relly sorry for asking you again and again but... GROMACS: gmx distance, VERSION 5.1.4 Executable: /usr/local/gromacs/bin/gmx Data prefix: /usr/local/gromacs Command line: gmx distance -n index.ndx -f conf0.gro -select 'com of group 2 plus com of group 6'
------------------------------------------------------- Program: gmx distance, VERSION 5.1.4 Source file: src/gromacs/trajectoryanalysis/runnercommon.cpp (line 300) Function: void gmx::TrajectoryAnalysisRunnerCommon::initTopology(gmx::SelectionCollection*) Inconsistency in user input: No topology provided, but one is required for analysis For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- Whai is the problem?;( On Sat, Jan 13, 2018 at 4:05 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/11/18 11:38 AM, rose rahmani wrote: > >> [ ZnS ] >> 1 2 3 4 5 6 7 8 9 10 11 12 13 14 >> 15 >> 16 17 18 19 20 21 22 23 24 25 26 27 28 29 >> 30 >> 31 32 33 34 35 36 37 38 39 40 41 42 43 44 >> 45.............. >> >> [ Protein ] >> 761 762 763 764 765 766 767 768 769 770 771 772 773 774 >> 775 >> 776 777 778 779 780 781 782 783 784 785 786 >> >> command; gmx distance -n index.ndx -f conf0.gro -select 'com of group >> "ZnS" >> plus com of group "Protein"' -oxyz -oall >> i exactly select index groups!!! >> ------------------------------------------------------- >> Program: gmx distance, VERSION 5.1.4 >> Source file: src/gromacs/selection/selectioncollection.cpp (line 616) >> Function: void gmx::SelectionCollection::setI >> ndexGroups(gmx_ana_indexgrps_t*) >> >> Inconsistency in user input: >> Invalid index group reference(s) >> Cannot match 'group "ZnS"', because no such index group can be found. >> Cannot match 'group "Protein"', because no such index group can be >> found. >> >> For more information and tips for troubleshooting, please check the >> GROMACS >> website at http://www.gromacs.org/Documentation/Errors >> ------------------------------------------------------------ >> --------------------------------- >> so i had to use this command; gmx distance -n index.ndx -f conf0.gro >> -select -oxyz >> GROMACS: gmx distance, VERSION 5.1.4 >> Executable: /usr/local/gromacs/bin/gmx >> Data prefix: /usr/local/gromacs >> Command line: >> gmx distance -n index.ndx -f conf0.gro -select -oxyz >> >> Available static index groups: >> Group 0 "System" (4336 atoms) >> Group 1 "Other" (760 atoms) >> Group 2 "ZnS" (560 atoms) >> Group 3 "WAL" (200 atoms) >> Group 4 "NA" (5 atoms) >> Group 5 "CL" (5 atoms) >> Group 6 "Protein" (26 atoms) >> Group 7 "Protein-H" (12 atoms) >> . >> . >> (one per line, <enter> for status/groups, 'help' for help, Ctrl-D to end) >> >>> 2 >>> >> Selection '2' parsed >> >>> 6 >>> >> Selection '6' parsed >> > > You should be selecting 'com of group 2' etc. here to get what you want. I > don't know why the command-line version of this didn't work, but to get a > COM distance, you need to tell gmx distance to do it, otherwise it's just > going to produce pairwise distances, which is what you're asking for here. > > -Justin > > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Assistant Professor > Virginia Tech Department of Biochemistry > > 303 Engel Hall > 340 West Campus Dr. > Blacksburg, VA 24061 > > jalem...@vt.edu | (540) 231-3129 > http://www.biochem.vt.edu/people/faculty/JustinLemkul.html > > ================================================== > > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support > /Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.