[gmx-users] Re: gmx FF with hydrogens for NMR stuff

[Alan Wilter Sousa da Silva]

Hi!

Not a PDB file format error. I'm still trying.
I did, for speptide.pdb form gmx tutorial:

FF=5
pdb2gmx -f speptide.pdb -p speptide.top -o speptide.gro <<EOF
$FF
EOF
editconf -f speptide -o -d 0.5 #(not -dc anymore)
genbox -cp out -cs -p speptide -o b4em
grompp -v -f em -c b4em -o em -p speptide
mdrun -v -s em -o em -c after_em -g emlog

OUTPUT:

checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 1232 of the 1431 non-bonded parameter combinations
Cleaning up temporary file gromppz0R7Np
Fatal error: Atomtype 'K' not found!

With FF = 0, 1, 2, 3 and 4 everything works fine!

So?

Cheers,
Alan

On Wed, 12 Jan 2005, Alan Wilter Sousa da Silva wrote:
> Despite what said (Do NOT use for new runs), I'm trying to do a MD with
> option 5 FF from pdb2gmx. Whatever I do I stop with a grompp error:
>
> Generated 1232 of the 1431 non-bonded parameter combinations
> Cleaning up temporary file gromppnoq8ef
> Fatal error: Atomtype 'K' not found!
>
> I would thank any advice here.

--------------------------
Alan Wilter Sousa da Silva
--------------------------
D.Sc. - IBCCF/UFRJ
Projeto BioPAUA - HP/LNCC
Petrópolis (RJ), Brasil
www.lncc.br/~alan