[gmx-users] methanol simulation error

[Mark Abraham]

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 
[molecules] section.

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.

Mark