On 1/2/16 9:43 AM, Nikhil Maroli wrote:
Dear all, im following US tutorial, in my topology ligand as LIG and Protein as Protein_Chain A,i made an index file by selecting Protein and LIG and changed in pull_md.mdp file in these entry entry pull_group1_name = Protein pull_group2_name = LIG gmx mdrun -s pull.tpr is completed successfully and i made several conf(i) files,when i execute perl script it shows following error Inconsistency in user input: Invalid index group reference(s) Cannot match 'group "Protein"', because no such index group can be found. Cannot match 'group "LIG"', 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 ------------------------------------------------------- Error: Multiple groups 'Protein' selected Error: Multiple groups 'LIG' selected i checked the index file which contains Protein and LIG Can anyone tell me where i made a mistake, i have visualized to make sure im pulling ligand and found it is correct,i made the change in script as Protein and LIG respectively *Later i changed Protein to Chain_A and LIG to Chain_B in index file and run the simulation ,script ends with an error* Program: gmx distance, VERSION 5.0.2 Source file: src/gromacs/selection/selectioncollection.cpp (line 581) Function: void gmx::SelectionCollection::setIndexGroups(gmx_ana_indexgrps_t*) Inconsistency in user input: Invalid index group reference(s) readline() on closed filehandle IN at distances.pl line 16. Use of uninitialized value $distance in concatenation (.) or string at distances.pl line 30. Group 'Chain_A' cannot be used in selections except as a full value of the selection, because atom indices in it are not sorted and/or it contains duplicate atoms. For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- 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. 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. ------------------------------------------------------- Program: gmx distance, VERSION 5.0.2 Source file: src/gromacs/selection/selectioncollection.cpp (line 581) Function: void gmx::SelectionCollection::setIndexGroups(gmx_ana_indexgrps_t*) Inconsistency in user input: Invalid index group reference(s) Group 'Chain_A' cannot be used in selections except as a full value of the selection, because atom indices in it are not sorted and/or it contains duplicate atoms.
Something is wrong with your index file relative to the way you are calling gmx distance. Diagnose without the script; all it does is loop over calls to gmx distance and assemble a summary file for you. Run the command interactively and figure out what groups you need to select.
-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.
