[gmx-users] problems in setup the protein+ membrane

[Mark Abraham]

On 12/02/10 12:16, chiloo777 777 wrote:
> Dear all,
>
> I face some problem during run grompp (see below), the command is
> "grompp -f em.mdp -c ../2add_lipw/b4ion.gro -p ../topol.top -o b4ion.tpr"
>
> -Before this process, i've changed the ffG53a6nb.itp&  ff53Ga6bon.itp
> according to the tutorial
> (http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/02_topology.html)
>
> my topology, you can see the attached files.
> Thanks in advance
> Jit
>
>
>
> --------------------------------------------------------------------------------------------
> Ignoring obsolete mdp entry 'cpp'
>
> Back Off! I just backed up mdout.mdp to ./#mdout.mdp.6#
> checking input for internal consistency...
> processing topology...
> Opening library file /usr/local/gromacs/share/top/ff_dum.itp
> Generated 825 of the 2346 non-bonded parameter combinations
>
> ERROR 1 [file /home/jit/Lipid_Bilayers/pope.itp, line 234]:
>    No default Proper Dih. types

If there's no default proper dihedral types defined, then you've 
#included things in a wrong order.

Mark

>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: toppush.c, line: 947
>
> Fatal error:
> Atomtype HO not found
> -------------------------------------------------------
>
> "There's Nothing We Can't Fix, 'coz We Can Do It in the Mix" (Indeep)
>
>