[gmx-users] US perl scripts fails index error

[Nikhil Maroli]

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.



-- 
Ragards,
Nikhil Maroli