Subashini .K subashinik at hotmail.com
Fri Jan 13 04:02:58 CET 2017

Hi gromacs users,

I am working on protein-ligand simulation..The commands were given in the following order


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


acpype -p com_solvated.top -x com_solvated.crd -b complex

After the following grompp command,

 gmx grompp -f em.mdp -c complex_GMX.gro -p complex_GMX.top -o em


; 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 groupnames, in which case you must supply an index file to the '-n' option
of grompp.


NOTE 1 [file complex_GMX.top, line 77775]:
  System has non-zero total charge: -0.000243
  Total charge should normally be an integer.

How can I fix the error? What commands should be given? Please help.

The protein was rec.pdb and ligand was lig.mol2

Where to spot the names in the .GRO file for energy-grps


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