[gmx-users] (no subject)

Mark Abraham Mark.Abraham at anu.edu.au
Sat Mar 3 01:05:59 CET 2007

maite lopez wrote:

Please use a helpfully descriptive subject line. Otherwise, thanks for 
the full description of what you've attempted to do.

> 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

You aren't generating a peptide_moved.itp file in the above.

> 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"

Look at lipid.itp line 8 - grompp thinks you can't use this directive 
there. That probably means you've made a typo in a previous directive 
that has only been noticed now. Check back through the #included .itp 
files for the error.


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