[gmx-users] methanol simulation error
Mark.Abraham at anu.edu.au
Fri Jan 7 02:41:27 CET 2011
On 7/01/2011 12:31 PM, 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 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.
I'm not sure why I'm repeating myself, but the name given in that
moleculetype is not SOL. That name must match what appears in the
Please make sure you have read the examples in Chapter 5 of the manual
and understand everything there.
> Please don't suggest non-water solvation in how-to part of Gromacs web.
> Could you tell me what missing is?
You're using atomtype CMET somewhere in your .top or its #included .itp
files. Your forcefield doesn't define atomtype CMET, and it needs to if
your usage is correct. Without seeing your topology, we can't say more.
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