[gmx-users] multiple groups selected error

[ashutosh srivastava]

Hi everyone

Still waiting for some solution. Any help regarding this would be
appreciated.

Best Regards

On Wed, Feb 15, 2017 at 11:50 AM, ashutosh srivastava <ashu4487 at gmail.com>
wrote:

> Hi
>
> My system contains protein, ligand (MOL) bound to protein, water(tip3p), 1
> Na and 1 Cl.
> Following is the command and output
>
> GROMACS:      gmx hbond, VERSION 5.1.2
> Executable:   /home/ashutosh/softwares/gromacs5/bin/gmx
> Data prefix:  /home/ashutosh/softwares/gromacs5
> Command line:
>   gmx hbond -f traj.xtc -s struct.tpr -num -g -dist -ang -hbn -hbm -life
> -tu ns -b 0 -e 2
>
> Reading file struct.tpr, VERSION 5.1.2 (single precision)
> Specify 2 groups to analyze:
> Group     0 (         System) has 58866 elements
> Group     1 (        Protein) has  5580 elements
> Group     2 (      Protein-H) has  2817 elements
> Group     3 (        C-alpha) has   334 elements
> Group     4 (       Backbone) has  1002 elements
> Group     5 (      MainChain) has  1337 elements
> Group     6 (   MainChain+Cb) has  1656 elements
> Group     7 (    MainChain+H) has  1659 elements
> Group     8 (      SideChain) has  3921 elements
> Group     9 (    SideChain-H) has  1480 elements
> Group    10 (    Prot-Masses) has  5580 elements
> Group    11 (    non-Protein) has 53286 elements
> Group    12 (            Ion) has     2 elements
> Group    13 (             NA) has     1 elements
> Group    14 (            MOL) has    40 elements
> Group    15 (             CL) has     1 elements
> Group    16 (          Water) has 53244 elements
> Group    17 (            SOL) has 53244 elements
> Group    18 (      non-Water) has  5622 elements
> Group    19 (          Other) has    40 elements
> Group    20 (             NA) has     1 elements
> Group    21 (            MOL) has    40 elements
> Group    22 (             CL) has     1 elements
> Group    23 ( Water_and_ions) has 53246 elements
> Select a group: Error: Multiple groups 'MOL' selected
> Error: No such group 'MOL'
> Select a group: Selected 17: 'SOL'
> Select a group:
> -------------------------------------------------------
> Program gmx hbond, VERSION 5.1.2
> Source code file: /home/ashutosh/softwares/gromacs-5.1.2/src/gromacs/topology/index.cpp,
> line: 917
>
> Fatal error:
> Cannot read from input
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
>
> Thank you
>
> Best Regards
> Ashutosh
>
> On Wed, Feb 15, 2017 at 11:09 AM, Mark Abraham <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> This was thought fixed some time ago. What is in your system that means
>> such groups are produced? Please share your terminal output.
>>
>> Mark
>>
>> On Wed, Feb 15, 2017 at 1:48 AM ashutosh srivastava <ashu4487 at gmail.com>
>> wrote:
>>
>> > Hi everyone
>> >
>> > I have written a python script that takes ligand group name as input and
>> > then does some analysis. However, the default groups that come out have
>> > repeated instances of ligand name and ions. Upon giving the ligand name
>> as
>> > argument it throws following error.
>> > Error: Multiple groups 'MOL' selected
>> > I am using Gromacs version 5.1.2
>> > I see that this was discussed a few years back (
>> >
>> > http://gmx-developers.gromacs.narkive.com/0d9veNZX/strange-d
>> efault-group-behavior
>> > )
>> > The possible workaround given in that thread- "to use the index
>> number", is
>> > not feasible for me here as the index group number for the ligand
>> changes
>> > in different simulations that I am analyzing. I would like to be able to
>> > use the ligand name for group selection.
>> > Is there any solution?
>> >
>> > Thank you
>> >
>> > Best Regards
>> > Ashutosh
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