[gmx-users] grompp error!
Florian Haberl
Florian.Haberl at chemie.uni-erlangen.de
Thu Dec 29 15:10:59 CET 2005
hi
On Thursday 29 December 2005 14:30, Rahul Karyappa wrote:
> Dear all,
>
> This is my topology file. When I run grompp command it gives me following error :
>
> Fatal error: number of coordinates in coordinate file (out.gro, 7048)does not match topology (topol1.top, 0).
It seems that you took the wrong top file, the number behind the filename means the atoms in the file and your topol1.top
contains zero.
>
>
> My .top file is as follows:
>
> Please help me out. Thanking you in advance.
>
>
> Rahul Karyappa
>
>
>
> ; forcefield parameters
>
> [ defaults ]
>
> ; nbfunc
> comb-rule
> gen-pairs fudgeLJ fudgeQQ
>
> 1
> 1
> no
> 1.0 1.0
>
>
> [ atomtypes ]
>
> ;name
> mass charge
> ptype
> c6 c12
>
> OM
> 15.99940
> -0.736 A
> 0.22617E-02 0.74158E-06
>
> S
> 32.06000
> +1.751 A
> 0.99844E-02 0.13078E-04
>
> OS
> 15.99940
> -0.736 A
> 0.22617E-02 0.74158E-06
>
> HC
> 1.00800
> 0.000 A
> 0.0 0.0
>
> C2
> 12.01100
> 0.000 A
> 0.90975E-02 0.35333E-04
>
> C3
> 12.01100
> 0.000 A
> 0.88765E-02 0.26150E-04
>
> OW
> 15.99940
> -0.820 A
> 0.26171E-02 0.26331E-05
>
> HW
> 1.00800
> 0.410 A
> 0.00000E+00 0.00000E+00
>
> Na
> 22.98980
> +1.000 A
> 0.72059E-04 0.21014E-07
>
> CR6
> 12.01100
> 0.000 A
> 0.55132E-02 0.15120E-04
>
> Mg
> 24.3050
> +1.100 A
> 0.72059E-04 0.21014E-07
>
> OY1 15.99940
> -0.550 A
> 0.26171E-02 0.26331E-05
>
> OY2 15.99940
> -0.550 A
> 0.26171E-02 0.26331E-05
>
> OY3 15.99940
> -0.550 A
> 0.26171E-02 0.26331E-05
>
> OY4 15.99940
> -0.758 A
> 0.26171E-02 0.26331E-05
>
> OY5 15.99940
> -0.758 A
> 0.26171E-02 0.26331E-05
>
> OY6 15.99940
> -0.792 A
> 0.26171E-02 0.26331E-05
>
> OY7 15.99940
> -0.867 A
> 0.26171E-02 0.26331E-05
>
> OY8 15.99940
> -0.867 A
> 0.26171E-02 0.26331E-05
>
> OY9 15.99940
> -0.683 A
> 0.26171E-02 0.26331E-05
>
> AL1
> 26.9815
> +1.450 A
> 0.72059E-04 0.21014E-07
>
> SI1
> 28.0855
> +1.100 A
> 0.72059E-04 0.21014E-07
>
> SI2
> 28.0855
> +1.100 A
> 0.72059E-04 0.21014E-07
>
> H1
> 1.00800
> 0.200 A
> 0.0 0.0
>
>
>
>
> [ nonbond_params ]
>
> ; i j
> func
> c6 c12
>
> OM OW 1 0.24329E-02 0.29873E-05
>
> OM Na 1 0.40370E-03 0.44478E-06
>
> OS Na 1 0.40370E-03 0.17791E-06
>
> OW OS 1 0.24329E-02 0.19915E-05
>
> CR6 CR6 1 0.0 0.0
>
>
> [ pairtypes ]
>
> ; i j
> func
> cs6 cs12
>
> OM C2 1 0.32685E-02 0.22969E-05
>
> OM OS 1 0.22617E-02 0.74158E-06
>
> OM S 1 0.47520E-02 0.31143E-05
>
> C2 S 1 0.68675E-02 0.96461E-05
>
> C2 OS 1 0.32685E-02 0.22969E-05
>
> C2 C2 1 0.47236E-02 0.71145E-05
>
> C2 C3 1 0.56894E-02 0.92642E-05
>
> ; Added manually
>
> HC C2 1 0.0 0.0
>
> HC C3 1 0.0 0.0
>
> HC OS 1 0.0 0.0
>
> HC S 1 0.0 0.0
>
> HC OM 1 0.0 0.0
>
>
> [ bondtypes ]
>
> ; i j
> func
> b0 kb
>
> S OM 1 0.15000 376560.
>
> S OS 1 0.15000 376560.
>
> OS C2 1 0.14300 251040.
>
> C2 C2 1 0.15300 334720.
>
> C3 C2 1 0.15300 334720.
>
> C2 HC 1 0.10900 292880.
>
> C3 HC 1 0.10900 292880.
>
> CR6 CR6 1 0.14120 600000.
>
>
> [ angletypes ]
>
> ; i j k
> func
> tHC cth
>
> OM S OM 1 109.500 500.080
>
> OM S OS 1 109.500 500.080
>
> S OS C2 1 120.000 397.480
>
> OS C2 C2 1 107.900 460.240
>
> C2 C2 C2 1 111.000 460.240
>
> C2 C2 C3 1 111.000 460.240
>
> HC C2 HC 1 109.500 292.880
>
> C2 C2 HC 1 109.500 292.880
>
> C3 C2 HC 1 109.500 292.880
>
> C2 C3 HC 1 109.500 292.880
>
> OS C2 HC 1 109.500 292.880
>
> HC C3 HC 1 109.500 292.880
>
>
> [ dihedraltypes ]
>
> ; i l
> func
> q0 cq
>
> S OS
> 1 0.000
> 3.766 3
>
> OS C2
> 1 0.000
> 3.766 3
>
> C2 C2
> 1 0.000
> 5.858 3
>
> C2 C3
> 1 0.000
> 5.858 3
>
>
>
> [ dihedraltypes ]
>
> C2 C2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495
>
>
>
>
>
>
> ; Include various molecular topologies
>
> #include "1unk.itp"
>
> #include "spc.itp"
>
> #include "1sds.itp"
>
>
> [ system ]
>
> ; Name
>
> unk in water
>
>
> [ molecules ]
>
> ; Compound #mols
>
> unk 1
>
> Na 16
>
> SOL 2148
>
>
Greetings,
Florian
--
-------------------------------------------------------------------------------
Florian Haberl
Computer-Chemie-Centrum
Universitaet Erlangen/ Nuernberg
Naegelsbachstr 25
D-91052 Erlangen
Mailto: florian.haberl AT chemie.uni-erlangen.de
-------------------------------------------------------------------------------
More information about the gromacs.org_gmx-users
mailing list