[gmx-users] methanol simulation error

Justin A. Lemkul jalemkul at vt.edu
Fri Jan 7 02:39:13 CET 2011

mustafa bilsel wrote:
> 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 will assume you're not using the current version of Gromacs.  This was a bug 
that was fixed some time ago.  Please upgrade to version 4.5.3.

> I have used grep to count the methanol molecules and added SOL 660 
> comment in .top file to tell the number of methanols.

Is SOL the appropriate name given in the [moleculetype] directive for methanol? 
  The name "SOL" is the default name for water in Gromacs, so this may be where 
you're having problems.  Just because methanol is a solvent doesn't mean it 
should be named SOL.  Check the name in the topology to be sure this is what you 
should be using.


> 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
> mustafa


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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