[gmx-users] grompp error!
Rahul Karyappa
r.karyappa at ncl.res.in
Thu Dec 29 14:30:44 CET 2005
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).
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
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