[gmx-users] Invalid order for directive defaults

Raghunadha Reddy Burri burri at heineken.chemie.uni-dortmund.de
Fri Dec 12 16:21:01 CET 2003


Dear GMX users  and David,

I am getting a simple error, please help me to run sucessfully in my peptide 
with tip5p water. Error details

Fatal error: Invalid order for directive defaults, file ""tip5p.itp"", line 1

I am attaching my tip5p.itp file (downloaded from David mail)

and

My process step by step.


pdb2gmx -f -ignh -ter -missing peptide.pdb -o peptide.gro -p peptide.top
5
3
3

editconf -bt cubic -f peptide.gro -o peptide.gro -c -d 0.7

genbox -cp peptide.gro -cs tip5p145.gro -o peptide_b4em.gro -p peptide.top


#editing peptide.top


grompp -f em.mdp -c peptide_b4em.gro -p peptide.top -o peptide_em.tpr



creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.5#
Warning: as of GMX v 2.0 unit of compressibility is truly 1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Generated 241860 of the 241860 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 241860 of the 241860 1-4 parameter combinations
Cleaning up temporary file gromppKp7rJA
Fatal error: Invalid order for directive defaults, file ""tip5p.itp"", line 1


Thank you for your time and consideration

Bye

RB
-------------- next part --------------
[ defaults ]
; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
1               3               yes             0.5     0.5

[ atomtypes ]
;name        mass      charge   ptype    sigma          epsilon
   OW    15.99940       0.000       A   3.12e-01      6.6944e-01
   HW     1.00800       0.000       A   0.00000E+00   0.00000E+00
   OL     0.000        -0.241       D   0.00000E+00   0.00000E+00

[ moleculetype ]
; molname       nrexcl
SOL             1

#define MNO
#ifdef MNO
; We use a strange order of atoms to make things go faster in GROMACS
[ atoms ]
; id    at type res nr  residu name     at name         cg nr   charge
1       HW      1       SOL             HW1             1       0.241
2       HW      1       SOL             HW2             1       0.241
3       OL      1       SOL             OL1             1      -0.241
4       OL      1       SOL             OL2             1      -0.241
5       OW      1       SOL              OW             1       0

[ constraints ]
; i     j       funct   distance
1       5       1       0.09572=20
2       5       1       0.09572=20
1       2       1       0.15139

[ dummies3 ]
; The position of the dummy is computed as follows:
;
; The distance from OW to OL is 0.07 nm, the geometry is tetrahedral
; (109.47 deg)
; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 |
;            c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 |
;           =20
;
; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2)
;       | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2)
; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31)

; Dummy from                    funct   a       b               c
4       5       1       2       4       -0.344908  -0.344908  -6.4437903493
3       5       1       2       4       -0.344908  -0.344908   6.4437903493

[ exclusions ]
1       2       3       4       5
2       1       3       4       5
3       1       2       4       5
4       1       2       3       5
5       1       2       3       4

#else

[ atoms ]
; id    at type res nr  residu name     at name         cg nr   charge
1       OW      1       SOL              OW             1       0
2       HW      1       SOL             HW1             1       0.241
3       HW      1       SOL             HW2             1       0.241
4       OL      1       SOL             OL1             1      -0.241
5       OL      1       SOL             OL2             1      -0.241

[ settles ]
; i     funct   doh     dhh
1       1       0.09572 0.15139

[ dummies3 ]
; The position of the dummy is computed as follows:
;
; The distance from OW to OL is 0.07 nm, the geometry is tetrahedral
; (109.47 deg)
; Therefore, a =3D b =3D 0.07 * cos (109.47/2) / | xOH1 + xOH2 |
;            c =3D 0.07 * sin (109.47/2) / | xOH1 X xOH2 |
;           =20
;
; Using | xOH1 X xOH2 | =3D | xOH1 | | xOH2 | sin (H1-O-H2)
;       | xOH1 + xOH2 | =3D 2 | xOH1 | cos (H1-O-H2)
; Dummy pos x4 =3D x1 + a*x21 + b*x31 + c*(x21 X x31)

; Dummy from                    funct   a       b               c
4       1       2       3       4       -0.344908  -0.344908  -6.4437903493
5       1       2       3       4       -0.344908  -0.344908   6.4437903493

[ exclusions ]
1       2       3       4       5
2       1       3       4       5
3       1       2       4       5
4       1       2       3       5
5       1       2       3       4
#endif


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