[gmx-users] REGARDING PROTEIN LIGAND SIMULATION

[Justin Lemkul]

On 1/12/17 10:02 PM, Subashini .K wrote:
> Hi gromacs users,
>
>
> I am working on protein-ligand simulation..The commands were given in the following order
>
> (1)
>
>
> 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
>
> (2)
>
> acpype -p com_solvated.top -x com_solvated.crd -b complex
>
>
> After the following grompp command,
>
> (3)
>  gmx grompp -f em.mdp -c complex_GMX.gro -p complex_GMX.top -o em
>
> where
> #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 = 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.
>
>
> and
>
> 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.
>

http://www.gromacs.org/Documentation/Floating_Point_Arithmetic

> The protein was rec.pdb and ligand was lig.mol2
>
> Where to spot the names in the .GRO file for energy-grps
>

I've already answered this twice.  See my latest reply from this morning for detail.

-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

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