[gmx-users] (no subject)

maite lopez lopezmai at gmail.com
Fri Mar 2 22:15:01 CET 2007

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
 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
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
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

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"

; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000

; 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.


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