Hi Replace the name of groups in original script by the names in between which you want to measure the distance
Good luck! On Dec 1, 2017 5:50 PM, "Kingsley Theras Primus Dass ." < 105726...@gms.tcu.edu.tw> wrote: > dear users, > I am encountering a problem with script, the summary.dat file does > not generate > any value. But if I run the distance command one at the time , it is > generating the value, I could not figure out where I am goingperlgmx wrong. > can anyone tell where lies the mistake?mistake? > > > Thank you > > *below the command line for one distance * > Command line: > gmx_mpi distance -s sgdp_pull_t.tpr -f conf1.pdb -n index.ndx -oall > dist1.xvgtpr -f conf1.pdb -n index.ndx -oall dist1.xvg -n index. - > dist1.xvg > pdbndxoall > > Available static index groups: > Group 0 "System" (89993 atoms) > Group 1 "Protein" (6541 atoms) > Group 2 "Protein-H" (5087 atoms) > Group 3 "C-alpha" (644 atoms) > Group 4 "Backbone" (1932 atoms) > Group 5 "MainChain" (2578 atoms) > Group 6 "MainChain + Cb" (3192 atoms) > Group 7 "MainChain + H" (3209 atoms) > Group 8 "SideChain" (3332 atoms) > Group 9 "SideChain-H" (2509 atoms) > Group 10 "Prot-Masses" (6541 atoms) > Group 11 "non-Protein" (83452 atoms) > Group 12 "Other" (12949 atoms) > Group 13 "_ *" (19 atoms) > Group 14 "GDP" (34 atoms) > Group 15 "POPC" (12896 atoms) > Group 16 "NA" (107 atoms) > Group 17 "CL" (106 atoms) > Group 18 "Water" (70290 atoms) > Group 19 "SOL" (70290 atoms) > Group 20 "non-Water" (19703 atoms) > Group 21 "Ion" (213 atoms) > Group 22 "_ *" (19 atoms) > Group 23 "GDP" (34 atoms) > Group 24 "POPC" (12896 atoms) > Group 25 "NA" (107 atoms) > Group 26 "CL" (106 atoms) > Group 27 "Water_and_ions" (70503 atoms) > Group 28 "Protein_chain_A" (3536 atoms) > Specify any number of selections for option 'select' > (Position pairs to calculate distances for): > (one per line, <enter> for status / groups, 'help' for help, Ctrl-D to end) > > > Reading file sgdp_pull_t.tpr, VERSION 5.1.4 (single precision) > Reading file sgdp_pull_t.tpr, VERSION 5.1.4 (single precision) > Reading frame 0 time 10.000 '', 89993 atoms > Last frame 0 time 10.000 > Analyzed 1 frames, last time 0.000 > GDP: > Number of samples: 17 > Average distance: 0.16202 nm > Standard deviation: 0.05626 nm > Protein_chain_A: > Number of samples: 1768 > Average distance: 0.19869 nm > Standard deviation: 0.12505 nm > > > > the error message that I get when I run perl script perl script > > readline () on closed filehandle IN at distances.pl line 16. > Use of uninitialized value $ distance in concatenation (.) Or string at > distances.pl line 30. > readline () on closed filehandle IN at distances.pl line 16. > Use of uninitialized value $ distance in concatenation (.) Or string at > distances.pl line 30. > readline () on closed filehandle IN at distances.pl line 16. > Use of uninitialized value $ distance in concatenation (.) Or string at > distances.pl line 30. > readline () on closed filehandle IN at distances.pl line 16. > Use of uninitialized value $ distance in concatenation (.) Or string at > distances.pl line 30. > readline () on closed filehandle IN at distances.pl line 16. > Use of uninitialized value $ distance in concatenation (.) Or string at > distances.pl line 30. > readline () on closed filehandle IN at distances.pl line 16. > Use of uninitialized value $ distance in concatenation (.) Or string at > distances.pl line 30. > readline () on closed filehandle IN at distances.pl line 16. > Use of uninitialized value $ distance in concatenation (.) Or string at > distances.pl line 30. > readline () on closed filehandle IN at distances.pl line 16. > Use of uninitialized value $ distance in concatenation (.) Or string at > distances.pl line 30. > readline () on closed filehandle IN at distances.pl line 16. > Use of uninitialized value $ distance in concatenation (.) Or string at > distances.pl line 30. > readline () on closed filehandle IN at distances.pl line 16. > Use of uninitialized value $ distance in concatenation (.) Or string at > distances.pl line 30. > Cleaning up ... > > > > 2017-11-30 23:10 GMT+08:00 Amir Zeb <zebami...@gmail.com>: > > > Solved it, > > > > Thanks every one! > > > > Amir > > > > On Thu, Nov 30, 2017 at 5:06 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > > > > > > > > > On 11/30/17 4:04 AM, Rose wrote: > > > > > >> Till nowi think the only solution is to use gmx distance for each > > >> conf.gro files.then use perl script. > > >> don't forget to delete gmx distance line from script. > > >> > > > > > > Or run one instance of gmx distance manually to understand how to > > properly > > > use it, diagnose any problems in your selection, etc. and fix the > script. > > > There's no reason to reinvent the wheel, just modify the script > properly > > to > > > suit your needs. > > > > > > -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. > > > -- > 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.
