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
--
==================================================
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
jalem...@outerbanks.umaryland.edu | (410) 706-7441
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