[gmx-users] Lipid-protein force field problem.

zazeri zazeri at yahoo.com.br
Mon Jul 9 01:26:10 CEST 2007

Hi to all ! :D

I've been trying to work with membrane
DPPC+peptide+waters simulation.
Following the "example.top" from Tieleman's website,
I've done my topology as:

#include "ffgmx.itp"
#include "lipid.itp"
#include "dppc.itp"
#include "protein.itp" ;(inside it has been written
#include "ffG43a2.itp")
#include "ions.itp"

And I've found:
"Fatal error:
Found a second defaults directive, file "lipid.itp",
line 9".

When I comment the line 9 and execute grompp again:

WARNING 1 [file "lipid.itp", line 13]:
  Overriding atomtype LO
WARNING 12 [file "lipid.itp", line 24]:
  Overriding atomtype LC2

So I've decide to comment #include "lipid.itp" in the
topology file:

"Fatal error:
Invalid order for directive defaults, file
""ffG43a2.itp"", line 4".

I've tried several things such as to change the order
of includes, etc and nothing has solved the

Therefore I've decided to make a force field with
ffgmx's parameters (to describe the lipids
interactions) + 
ffg43a2's parameters (to describe the peptide
interactions). I've done the field following the

Interactions between:
lipid - lipid: gmx
lipid - water: gmx
lipid - protein: gmx
protein - water: 43a2
protein - protein: 43a2
lipid - ions: gmx
protein - ions: 43a2
ions - ions: gmx
ions - water: gmx
water - water: gmx

In the topology file I've written:
#include "ffG43a2mod.itp" ;(modified)
#include "dppc.itp"
#include "peptide.itp"
#include "spc.itp"
#include "ions.itp"

And I've had to face this error:
Generated 846 of the 2080 non-bonded parameter
WARNING 1 [file "dppc.itp", line 223]:
  No default Ryckaert-Bell. types, using zeroes
WARNING 12 [file "dppc.itp", line 234]:
  No default Ryckaert-Bell. types, using zeroes
WARNING 13 [file "dppc.itp", line 239]:
  No default Ryckaert-Bell. types, using zeroes
WARNING 24 [file "dppc.itp", line 250]:
  No default Ryckaert-Bell. types, using zeroes

I think that it happens because I didn't define the
"bonded parameters" from ffgmxbon.itp to
In afirmative case, how do I do to convert and include
them? Note it's not enough copy and paste! :P

As you can see, I've tried to apply all tips described
in the gmx-users list e other like to make a mixture
gmx-43a2 force field using brute force.

So please, what am I doing wrong?

Thank you in advance, Zaz.

Novo Yahoo! Cadê? - Experimente uma nova busca.

More information about the gromacs.org_gmx-users mailing list