[gmx-users] US perl scripts fails index error

[Justin Lemkul]

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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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