[gmx-developers] executing mdp file--error

[Justin Lemkul]

This is a usage question and is not related to development; I am CC'ing this 
over to gmx-users.  Please continue the discussion there.

On 1/11/17 8:40 AM, Kulkarni R 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
>

This is a simple syntactical error.  A # in GROMACS is a cpp macro.  A ; is a 
comment.  Here, grompp is flagging the fact that you've entered an invalid line 
in your input .mdp 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 *
>

You're telling grompp you want mdrun to compute interaction energies between 
"protein" and "LIG" but there is no such thing as "LIG" in the system.  Don't 
tell grompp to use groups that don't exist :)

-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

==================================================