[gmx-users] Reverse_MICELLE>Fatel error, moleculetype SOL is redefined
harichem12 at yahoo.com
Tue Jul 16 07:02:24 CEST 2013
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 :
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.
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