Oops,Sorrry. Sometimes big challenges make ones think hard and ignore obvious issues. Thank you so much Mr.justin and joao
On Sat, Jan 13, 2018 at 4:01 PM, João Henriques < joao.m.a.henriq...@gmail.com> wrote: > The output is very explicitly telling you what the problem is. You didn't > provide a topology. Pass one the the -s flag. How do you want the COM to > be computed when you're not providing any masses? > > J > > On Jan 13, 2018 9:19 AM, "rose rahmani" <rose.rhm...@gmail.com> wrote: > > > 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? 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