[gmx-users] ERROR IN GROMPP

[Justin Lemkul]

On 1/12/17 8:19 AM, Subashini .K wrote:
> Hi gromacs users,
>
>
> I got an error when the following command
>
>
>  gmx grompp -f em.mdp -c complex_GMX.gro -p complex_GMX.top -o em
>
>
> The corresponding em.mdp was
>
> ; 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 = receptor LIG
> cutoff-scheme = verlet
> vdw-type = cut-off
> rvdw = 1.0
> coulombtype = pme
> rcoulomb = 1.0
>
>
> The fatal error was
>
>
> (1) Group receptor 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.
>
>
> and
>
> NOTE 1 [file complex_GMX.top, line 77775]:
>   System has non-zero total charge: -0.000243
>   Total charge should normally be an integer.
>
>
>
>
> The previous commands were
>
>
> source leaprc.ff14SB
> loadAmberParams frcmod.tip4pew
> loadAmberParams frcmod.ionsjc_tip4pew
> source leaprc.gaff
> LIG = loadmol2 LIG.mol2
> loadamberparams LIG.frcmod
> check LIG
> receptor = loadPDB rec_final.pdb
> complex = combine {receptor LIG}
> set default PBRadii mbondi2
> saveAmberParm LIG LIG.top LIG.crd
> receptor = loadPDB rec_final.pdb
> saveAmberParm receptor rec.top rec.crd
> saveAmberParm complex com.top com.crd
> savepdb complex complex_gas.pdb
> charge complex
> addIons2 complex Na+ 0
> solvateBox complex TIP4PBOX 10.0
> saveAmberParm complex com_solvated.top com_solvated.crd
> savepdb complex com_solvated.pdb
> quit
>
>
> How can I fix the error? Please help.
>

grompp tells you this in the error message above.

> The protein was rec.pdb and
> ligand was lig.mol2
>
> What should be energy-grps = ??
>

energygrps allow for the decomposition of short-range nonbonded energy terms 
between whatever is specified.  Whether or not these values are at all 
meaningful can be questionable.  If you want an interaction energy and think 
it's useful, you need to specify valid names of either [moleculetype] entries or 
custom-named index groups (as grompp tells you in its error message).

-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

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