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

Hari Pandey harichem12 at yahoo.com
Tue Jul 16 07:02:24 CEST 2013

Hi Gromaxers,
Thanks for previous answers.
I have to simulate reverse micelle after solvation with isooctane.My system now is:


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 

Please advice me how do I do this.
Thanks for your help.

More information about the gromacs.org_gmx-users mailing list