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.
Mark
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