[gmx-developers] executing mdp file--error

[Erik Lindahl]

First, this isn't a development-related question, so please use gmx-users instead.

Second, the program tells you quite explicitly what the problems are and how to read up on it and rectify the issue. What happened when you tried to follow those instructions?

Cheers,

Erik

Erik Lindahl <erik.lindahl at scilifelab.se>
Professor of Biophysics
Science for Life Laboratory
Stockholm University & KTH
Office (SciLifeLab): +46 8 524 81567
Cell (Sweden): +46 73 4618050
Cell (US): +1 267 3078746


> On 11 Jan 2017, at 14:40, Kulkarni R <alumniphysics at hotmail.com> wrote:
> 
> Hi gromacs users,
> 
> 
> I am using Gromacs version 5.1.1 and em.mdp is 
> 
> 
> #em.mdp
> ; to test
> ; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
> ; mdrun -v -deffnm em
>  #Grompp minimization
> integrator = steep
> nsteps = 500
> nstlist = 10
> energy-grps = protein LIG
> cutoff-scheme = verlet
> vdw-type = cut-off
> #energy-grps = protein LIG
> rvdw = 1.0
> coulombtype = pme
> rcoulomb = 1.0
> 
> 
> While executing the following command through cgywin
> 
> GMX grompp -f em.mdp -c complex_GMX.gro -p complex_GMX.top -o em
>        
> 
> WARNING 1 [file em.mdp, line 16]:
>   Unknown left-hand '#energy-grps' in parameter file
> 
> 
> Setting the LD random seed to 2594680474
> Generated 861 of the 861 non-bonded parameter combinations
> Generating 1-4 interactions: fudge = 0.5
> Generated 861 of the 861 1-4 parameter combinations
> Excluding 3 bonded neighbours molecule type 'complex'
> Excluding 1 bonded neighbours molecule type 'CL-'
> Excluding 2 bonded neighbours molecule type 'WAT'
> 
> NOTE 1 [file complex_GMX.top, line 77771]:
>   System has non-zero total charge: -0.000243
>   Total charge should normally be an integer. See
>   http://www.gromacs.org/Documentation/Floating_Point_Arithmetic
>   for discussion on how close it should be to an integer.
> 
> 
> Cleaning up constraints and constant bonded interactions with virtual sites
> Removing all charge groups because cutoff-scheme=Verlet
> Analysing residue names:
> There are:   430    Protein residues
> There are:     1      Other residues
> There are:    38        Ion residues
> There are: 19837      Water residues
> Analysing Protein...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
> Analysing residues not classified as Protein/DNA/RNA/Water and splitting into groups...
> 
> -------------------------------------------------------
> Program gmx grompp, VERSION 5.1.1
> Source code file: /cygdrive/h/gromacs/gromacs-5.1.1/src/gromacs/gmxpreprocess/readir.c, line: 2585
> 
> Fatal error:
> Group LIG referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp.
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> 
> How to rectify the error 
> 
> * Group LIG referenced in the .mdp file was not found in the index file.
> Group names must match either [moleculetype] names or custom index group
> names, in which case you must supply an index file to the '-n' option
> of grompp *
> 
> Thanks,
> Kulkarni.R
> 
> 
> 
> 
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