[gmx-users] Invalid order for directive defaults

[David van der Spoel]

On Fri, 2003-12-12 at 16:20, Raghunadha Reddy Burri wrote:
> 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)
> 
this is a "standalone" topology file.
Actuallly tip5p is not really part of the OPLS force field it seems. It
could be made to, though.

Here goes:

insert these three lines in ffoplsaa.atp:
 opls_118   15.99940  ; O TIP5P Water
 opls_119    1.00800  ; H TIP5P Water
 opls_120    0.00000  ; L TIP5P Water

Insert the following lines in ffoplsaanb.itp:
 opls_118   OW     15.99940     0.000 A   3.12e-01      6.6944e-01
 opls_119   HW      1.00800     0.000 A   0.00000E+00   0.00000E+00
 opls_120   OL      0.000       0.000 D   0.00000E+00   0.00000E+00

And use the attached tip5p file

Updated tip4p and tip3p files are in gromacs 3.2.0beta, the new tip5p
stuff will be in the release.

> 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
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
-------------- next part --------------
;
; This topology file should work with ffoplsaa.itp
;

	
[ moleculetype ]
; molname       nrexcl
SOL             2

#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       opls_119     1       SOL             HW1             1       0.241
2       opls_119     1       SOL             HW2             1       0.241
3       opls_120     1       SOL             OL1             1      -0.241
4       opls_120     1       SOL             OL2             1      -0.241
5       opls_118     1       SOL              OW             1       0

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