[gmx-users] (no subject)

[Tsjerk Wassenaar]

Hi Maite,

I think the answer is in the archive. But first, could you please
state your question in the subject. Especially since you gave first a
listing of your output, it wasn't really helpful not having an idea
what to look for. I almost decided to ignore this mail...

But likely you have an #include statement in lipid.itp trying to
include ffgmx.itp or something of the like.

Tsjerk

On 3/2/07, maite lopez <lopezmai at gmail.com> wrote:
> Hi gromacs users:
>
> I am working on membrane peptides simulation under lipid (DPPC, from
> Peter Tieleman group site). I have downloaded the lipid and dppc .itp
> from
>  the same site.
> The steps that I am following are as follows and all my files are in
> the work directory:
>
> 1)pdb2gmx_331 -f peptide_moved.pdb -o peptide_moved.gro -p
> peptide_moved.top -i peptide_moved_posre.itp -ff G53a5 -water spc -ter
> -lys -asp -glu -ignh
> 2)editconf_331 -f dppc64.pdb -o dppc64.gro     (I changed DPPC x DPP
> and ATOM x HETATM)
> 3)cat peptide_moved.gro dppc64.gro > peptide_dppc64.gro  (I've edited this file)
> 4)editconf_331 -f peptide_dppc64.gro -o peptide_dppc64_edit.gro
> (reorder the atoms)
> 5)editconf_331 -f peptide_dppc64_edit.gro -o peptide_dppc64_box.gro
> -bt triclinic -c -box 4.725 4.232 12 (Creating the water
> box)
> 6)genbox_331 -cp peptide_dppc64_edit_box.gro -cs -o
> peptide_dppc64_water.gro -p peptide_dppc64.top (add water molecules)
>
> But..when I run grompp
> 7)grompp_331 -f peptide_dppc64_em.mdp -po peptide_dppc64_em_out.mdp -c
> peptide_dppc64_water.gro -p peptide_dppc64.top -o
> peptide_dppc64_em.tpr
>
> It gives
>
> Fatal error:
> Invalid order for directive defaults, file ""lipid.itp"", line 8
>
> this is my initial .top file
>
> ; Include forcefield parameters
> #include "ffG53a5.itp"
>
> ; Include chain topologies
> #include "peptide_moved.itp"
> #include "lipid.itp"
> #include "dppc.itp"
>
>
> ; Include water topology
> #include "spc.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> ; Include generic topology for ions
> #include "ions.itp"
>
> [ system ]
> ; name
> peptide StII-30 + dppc64
>
> [ molecules ]
> ; name  number
> Protein 1
> DPP     64
> SOL     5737
>
>
> I haven't include the forcefield twice and my protein.itp hasn't it.
>
> I've done many things as suggested in mailing list that I explain in
> other mail cos i don´t  send a  message body  bigger than 50Kb.
>
> Any help will be highly appreciated.
>
> Maite
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623