[gmx-users] Reverse_MICELLE>Fatel error, moleculetype SOL is redefined

Justin Lemkul jalemkul at vt.edu
Tue Jul 16 13:07:04 CEST 2013

On 7/16/13 1:02 AM, Hari Pandey wrote:
> Hi Gromaxers,
> Thanks for previous answers.
> I have to simulate reverse micelle after solvation with isooctane.My system now is:
> ISOOCTANE(solvent)+AOT(surfactant)+coreWATER.
> When I do grompp, it says moleculetype SOL is redefined and lots of another errors.
> Please advice me how do I do  reverse micelle simulation.
> What I did is::
> (1)   pdb2gmx -f RM.pdb -o RM.gro -p RM.top  step :::: I choose  isooctane as water model. I have isooctane.itp  in the file watermodel.dat inside my forcefield.
> (2)   editconf -c  -f   RM.gro  -o  RM1.gro -p RM.top -bt dodecahedron -d 2.0  -shell 0.3
> (3)  genbox  -cp RM.gro -cs isooctane.gro -p  reverse_RM.top -o RM2.pdb
> (4)  grompp -f  em.mdp -c RM2.pdb -p RM.top -n index.ndx -o em.tpr -maxwarn 5
> where RM.pdb is  pdb file of  reverse micelle
> All required files I have ,and I have index.ndx file also
> But it returns :
> Fatel error:
> the moleculetype  SOL is redefined
> I tried lots, I change the SOL to WATER every where in frocefield as well as my .gro file too. I tried all what I could but no get any benifit.  So

You have two topologies that define a [moleculetype] named SOL, which causes the 
error.  Likely it's somewhere in the isooctane.itp file, because you seem to be 
treating it like water above (which is unnecessary).



Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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