[gmx-users] multiple groups selected error

[ashutosh srivastava]

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-
> default-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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