[gmx-users] Invalid order for directive defaults

[Atila Petrosian]

Dear all

My system contains protein + cnt + water molecules.

I have summarized what I did below:
-----------------------------------------------------------------------------------

1) By pdb2gmx and charmm27 force field, I obtained pr.top for protein then
I converted it into pr.itp by deleting

; Include forcefield parameters
#include "charmm27.ff/forcefield.itp"

from begining of file and by deleting

; Include water topology
#include "charmm27.ff/tip3p.itp"

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

; Include topology for ions
#include "charmm27.ff/ions.itp"

[ system ]
; Name
Protein

[ molecules ]
; Compound        #mols
Protein_chain_A     1

from ending of file.
------------------------------------------------------------------------------------

2) I used bonded and nonbonded parameters for cnt from paper:
 J. Phys. Chem. B 2001, 105, 9980-9987
(Carbon Nanotubes in Water: Structural Characteristics and Energetics).
I created cnt.ff folder containing following files:

ffcnt.atp / ffcnt.n2t / ffcnt.rtp / ffcntbon.itp / ffcntnonbon.itp /
forcefield.itp

Then, I put cnt.ff folder in GMXLIB directory.
------------------------------------------------------------------------------------

3) By g_x2top and cnt.ff created in previous step, I obtained cnt.top for
cnt then I converted it into cnt.itp by deleting

; Include forcefield parameters
#include "cnt.ff/forcefield.itp"

from begining of file and by deleting

[ system ]
; Name
CNT

[ molecules ]
; Compound        #mols
CNT                 1

from ending of file.
------------------------------------------------------------------------------------

4) I combined cnt and protein to create one coordination file (system.gro).
Order of molecules are as follows: 1) cnt 2) protein
3) water.
------------------------------------------------------------------------------------

5) I wrote a topol.top file given below,

; Include forcefield parameters
#include "cnt.ff/forcefield.itp"

#include "cnt.itp"

#include "charmm27.ff/forcefield.itp"

#include "pr.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

; Include water topology
#include "charmm27.ff/tip3p.itp"

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

; Include topology for ions
#include "charmm27.ff/ions.itp"

[ system ]
; Name
CNT/Protein/SOL

[ molecules ]
; Compound        #mols
CNT          1
Protein      1
SOL       1359
------------------------------------------------------------------------------------

When I used grompp -f minim.mdp -c system.gro -p topol.top -o minim.tpr, I
encountered with following error:

Fatal error:
Syntax error - File forcefield.itp, line 11
Last line read:
'[ defaults ]'
Invalid order for directive defaults

Content of forcefield.itp in cnt.ff directory is as follows:

*******************************************************************************
*                    CHARMM port writted
by                                   *
*                    Par Bjelkmar, Per Larsson, Michel
Cuendet,               *
*                    Berk Hess and Erik
Lindahl.                              *
*
Correspondance:                                          *
*                    bjelkmar at cbr.su.se or lindahl at cbr.su.se
*
*******************************************************************************


#define _FF_CNT
[ defaults ]
; nbfunc    comb-rule    gen-pairs    fudgeLJ    fudgeQQ
1    2    yes    1.0    1.0

#include "ffcntnonbon.itp"
#include "ffcntbon.itp"

and

Content of forcefield.itp in Charmm27.ff directory is as follows:

*******************************************************************************
*                    CHARMM port writted
by                                   *
*                    Par Bjelkmar, Per Larsson, Michel
Cuendet,               *
*                    Berk Hess and Erik
Lindahl.                              *
*
Correspondance:                                          *
*                    bjelkmar at cbr.su.se or lindahl at cbr.su.se
*
*******************************************************************************


#define _FF_CHARMM
[ defaults ]
; nbfunc    comb-rule    gen-pairs    fudgeLJ    fudgeQQ
1    2    yes    1.0    1.0

#include "ffnonbonded.itp"
#include "ffbonded.itp"
#include "gb.itp"
#include "cmap.itp"
; Nucleic acids nonbonded and bonded parameters"
#include "ffnanonbonded.itp"
#include "ffnabonded.itp"
------------------------------------------------------------------------------------

In both of forcefield.itp files, line 11 is [ defaults ].

I changed name of  forcefield.itp file in cnt.ff directory to cntff.itp,
but there is same error, again.

That is all what I exactly did. Is anything wrong or missing?
How to solve this error?

Any help will highly appreciated