[gmx-developers] executing mdp file--error

[Kulkarni R]

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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