yes. 19 and 20. I have been able to modify distances.pl and it is running well I guess. It is taking a little time per configuration to process.
Is there any way to know if distances.pl program terminates normally and calculations are successful ? On Sun, Jan 8, 2017 at 2:20 AM, Justin Lemkul <jalem...@vt.edu> wrote: > > > On 1/7/17 3:36 PM, abhisek Mondal wrote: > >> Alright, I'm trying. >> Please tell me one thing, given the fact I want to analyse the >> protein-ligand pull scenario, what should be my choice during the prompt i >> get after executing "g_dist_mpi -s pull.tpr -f conf200.gro -n index.ndx -o >> all" >> >> Reading file pull.tpr, VERSION 4.6.2 (single precision) >> Group 0 ( System) has 2648311 elements >> Group 1 ( Protein) has 1693 elements >> Group 2 ( Protein-H) has 1301 elements >> Group 3 ( C-alpha) has 163 elements >> Group 4 ( Backbone) has 489 elements >> Group 5 ( MainChain) has 653 elements >> Group 6 ( MainChain+Cb) has 805 elements >> Group 7 ( MainChain+H) has 815 elements >> Group 8 ( SideChain) has 878 elements >> Group 9 ( SideChain-H) has 648 elements >> Group 10 ( Prot-Masses) has 1693 elements >> Group 11 ( non-Protein) has 2646618 elements >> Group 12 ( Other) has 15 elements >> Group 13 ( JZ4) has 15 elements >> Group 14 ( NA) has 1602 elements >> Group 15 ( CL) has 1608 elements >> Group 16 ( Water) has 2643393 elements >> Group 17 ( SOL) has 2643393 elements >> Group 18 ( non-Water) has 4918 elements >> Group 19 (Protein_chain_A) has 3210 elements >> Group 20 ( JZ4) has 15 elements >> Group 21 ( NA) has 1602 elements >> Group 22 ( CL) has 1608 elements >> Group 23 ( Water_and_ions) has 2646603 elements >> Group 24 ( r_1-163) has 5605 elements >> Group 25 ( r_164) has 39 elements >> >> Do I go with System ? I only need to see protein-ligand pull though. >> > > What groups defined your reaction coordinate for the pulling? Those are > the groups you want. > > -Justin > > > Can you give me some suggestions ? >> >> On Sun, Jan 8, 2017 at 1:58 AM, Justin Lemkul <jalem...@vt.edu> wrote: >> >> >>> >>> On 1/7/17 3:24 PM, abhisek Mondal wrote: >>> >>> So I'm supposed to run "g_dist_mpi", right ? I'm on gromacs-4.6.2. >>>> >>>> >>>> If you're using an old version, the syntax is totally different, so you >>> will have to make lots of changes to the script (or not use it at all). >>> >>> The catch here to analyze the COM distances between 2 pull groups. Am I >>> >>>> getting that right ? >>>> >>>> >>>> Yes. >>> >>> -Justin >>> >>> >>> On Sun, Jan 8, 2017 at 1:46 AM, Justin Lemkul <jalem...@vt.edu> wrote: >>> >>>> >>>> >>>> >>>>> On 1/7/17 2:51 PM, abhisek Mondal wrote: >>>>> >>>>> Hi, >>>>> >>>>>> I'm pulling ligand out of protein using umbrella sampling method in >>>>>> gromacs-4.6.2. >>>>>> Using "trjconv -s pull.tpr -f traj.xtc -o conf.gro -sep" command >>>>>> generated >>>>>> 500 different files (selected "SYSTEM" in interactive prompt, need to >>>>>> study >>>>>> protein and ligand simultaneously). But when I use "perl distances.pl >>>>>> " >>>>>> command I get none of the distances calculated. >>>>>> Following output was generated: >>>>>> >>>>>> ... >>>>>> Processing configuration 497... >>>>>> Processing configuration 498... >>>>>> Processing configuration 499... >>>>>> Processing configuration 500... >>>>>> 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. >>>>>> ... >>>>>> >>>>>> >>>>>> Help me out here. What did go wrong ? >>>>>> >>>>>> >>>>>> gmx distance failed. Run gmx distance yourself and see what the error >>>>>> >>>>> message is. The script just executes gmx distance and assumes >>>>> everything >>>>> works because it's designed for a tutorial. You may have to modify it >>>>> to >>>>> get it to work in your system; you can't assume it is plug-and-play. >>>>> >>>>> -Justin >>>>> >>>>> -- >>>>> ================================================== >>>>> >>>>> Justin A. Lemkul, Ph.D. >>>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>>>> >>>>> Department of Pharmaceutical Sciences >>>>> School of Pharmacy >>>>> Health Sciences Facility II, Room 629 >>>>> University of Maryland, Baltimore >>>>> 20 Penn St. >>>>> Baltimore, MD 21201 >>>>> >>>>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>>>> http://mackerell.umaryland.edu/~jalemkul >>>>> >>>>> ================================================== >>>>> -- >>>>> 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. >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>> ================================================== >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 629 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> ================================================== >>> -- >>> 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. >>> >>> >> >> >> > -- > ================================================== > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 629 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > ================================================== > -- > 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. > -- Abhisek Mondal *Research Fellow* *Structural Biology and Bioinformatics Division* *CSIR-Indian Institute of Chemical Biology* *Kolkata 700032* *INDIA* -- 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.