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
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