[gmx-users] methanol simulation error

mustafa bilsel mfbilsel at gmail.com
Fri Jan 7 02:31:40 CET 2011

Hi all,
I try to make a simulation in methanol. I use gromos43a1 forcefield.
My command follow,
pdb2gmx -f xxx.pdb
editconf -f conf.gro -bt dodecahedron -d 0.8 -o box.gro
genbox -cp box.gro -cs methanol216.gro -p topol.top -o solvated.gro
When  grompp for minimization it gives an error:
Atomtype CMET not found

I have used grep to count the methanol molecules and added SOL 660 comment
in .top file to tell the number of methanols.
Also I added #include "gromos43a1.ff/methanol.itp" line to .top.

Please don't suggest non-water solvation in how-to part of Gromacs web.

Could you tell me what missing is?

best wishes
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