[gmx-users] Re: Re: problems running grompp with protein-ligand complex

[Ragnarok sdf]

I am working with a system using ffamber99 forcefield and trying to
set up a ligand protein complex system. I have encountered some
problems with grompp now.
In my past email, the problem was that : > Fatal error: Found a second
defaults directive, file "ligand.itp", line 5. Then the following
solution was given:

" You have to combine all atomtypes into one file something like

filename ff_atomtypes.itp

#define FF_ATOMTYPES

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               2               yes             0.5     0.8333


[ atomtypes ]
; name        mass      charge    ptype               sigma
epsilon

     S       0.0000  0.0000  A   3.56359e-01  1.04600e+00
   CC      0.0000  0.0000  A   3.39967e-01  3.59824e-01
   HO      0.0000  0.0000  A   0.00000e+00  0.00000e+00
   N3      0.0000  0.0000  A   3.25000e-01  7.11280e-01
all atom types from amber force field 99 and also from your ligand (check if
parameters are ok).


delete atomtypes and defaults entry in your ligand.itp

load in your .top

#include "ff_atomtypes.itp"

#include "receptor.itp"
#include "ligand.itp"
"
I tried to do this and ended up with the following .top file:

; 15d-pgj2_GMX.top created by acpypi on Wed Dec  3 14:10:55 2008

[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               2               yes             0.5     0.8333

; Include 15d-pgj2_GMX.itp topology
#include "15d-pgj2_GMX.itp"

[ system ]
 15d-pgj2

[ molecules ]
; Compound        nmols
 15d-pgj2         1

And all the atomtypes are in the 15d-pgj2_GMX.itp, which is too big to
put here. But is present in past posts.
Ok, so no grompp tells me the same error it did before. Fatal error:
Found a second defaults directive, file "15d-pgj2_GMX.top"

When I substitute the 15d-pgj2_GMX.top for the 15d-pgj2_GMX.itp in my
protein.top grompp gives out the following error:

Fatal error:No such moleculetype PJ2

Now I am quite confused and would like some advice on the matter.
Thank you
Fabrício Bracht