[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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