<HTML><HEAD><META content="text/html; charset=x-user-defined" http-equiv="Content-Type"><style type="text/css"><!--.MailHeader { font-family: "Arial"; font-size: 8pt; color: #000000; font-style: normal; font-weight: normal; text-decoration: none; }//--></style></HEAD><BODY>Dear all,<br>
This is my topology file. When I run grompp command it gives me following error :<br>
Fatal error: number of coordinates in coordinate file (out.gro, 7048)does not match topology (topol1.top, 0).<br>
<br>
My .top file is as follows:<br>
Please help me out. Thanking you in advance.<br>
<br>
Rahul Karyappa<br>
<br>
<br>
; forcefield parameters<br>
[ defaults ]<br>
; nbfunc
comb-rule
gen-pairs fudgeLJ fudgeQQ<br>
1
1
no
1.0 1.0<br>
<br>
[ atomtypes ]<br>
;name
mass charge
ptype
c6 c12<br>
OM
15.99940
-0.736 A
0.22617E-02 0.74158E-06<br>
S
32.06000
+1.751 A
0.99844E-02 0.13078E-04<br>
OS
15.99940
-0.736 A
0.22617E-02 0.74158E-06<br>
HC
1.00800
0.000 A
0.0 0.0<br>
C2
12.01100
0.000 A
0.90975E-02 0.35333E-04<br>
C3
12.01100
0.000 A
0.88765E-02 0.26150E-04<br>
OW
15.99940
-0.820 A
0.26171E-02 0.26331E-05<br>
HW
1.00800
0.410 A
0.00000E+00 0.00000E+00<br>
Na
22.98980
+1.000 A
0.72059E-04 0.21014E-07<br>
CR6
12.01100
0.000 A
0.55132E-02 0.15120E-04<br>
Mg
24.3050
+1.100 A
0.72059E-04 0.21014E-07<br>
OY1 15.99940
-0.550 A
0.26171E-02 0.26331E-05<br>
OY2 15.99940
-0.550 A
0.26171E-02 0.26331E-05<br>
OY3 15.99940
-0.550 A
0.26171E-02 0.26331E-05<br>
OY4 15.99940
-0.758 A
0.26171E-02 0.26331E-05<br>
OY5 15.99940
-0.758 A
0.26171E-02 0.26331E-05<br>
OY6 15.99940
-0.792 A
0.26171E-02 0.26331E-05<br>
OY7 15.99940
-0.867 A
0.26171E-02 0.26331E-05<br>
OY8 15.99940
-0.867 A
0.26171E-02 0.26331E-05<br>
OY9 15.99940
-0.683 A
0.26171E-02 0.26331E-05<br>
AL1
26.9815
+1.450 A
0.72059E-04 0.21014E-07<br>
SI1
28.0855
+1.100 A
0.72059E-04 0.21014E-07<br>
SI2
28.0855
+1.100 A
0.72059E-04 0.21014E-07<br>
H1
1.00800
0.200 A
0.0 0.0<br>
<br>
<br>
[ nonbond_params ]<br>
; i j
func
c6 c12<br>
OM OW 1 0.24329E-02 0.29873E-05<br>
OM Na 1 0.40370E-03 0.44478E-06<br>
OS Na 1 0.40370E-03 0.17791E-06<br>
OW OS 1 0.24329E-02 0.19915E-05<br>
CR6 CR6 1 0.0 0.0<br>
<br>
[ pairtypes ]<br>
; i j
func
cs6 cs12<br>
OM C2 1 0.32685E-02 0.22969E-05<br>
OM OS 1 0.22617E-02 0.74158E-06<br>
OM S 1 0.47520E-02 0.31143E-05<br>
C2 S 1 0.68675E-02 0.96461E-05<br>
C2 OS 1 0.32685E-02 0.22969E-05<br>
C2 C2 1 0.47236E-02 0.71145E-05<br>
C2 C3 1 0.56894E-02 0.92642E-05<br>
; Added manually<br>
HC C2 1 0.0 0.0<br>
HC C3 1 0.0 0.0<br>
HC OS 1 0.0 0.0<br>
HC S 1 0.0 0.0<br>
HC OM 1 0.0 0.0<br>
<br>
[ bondtypes ]<br>
; i j
func
b0 kb<br>
S OM 1 0.15000 376560.<br>
S OS 1 0.15000 376560.<br>
OS C2 1 0.14300 251040.<br>
C2 C2 1 0.15300 334720.<br>
C3 C2 1 0.15300 334720.<br>
C2 HC 1 0.10900 292880.<br>
C3 HC 1 0.10900 292880.<br>
CR6 CR6 1 0.14120 600000.<br>
<br>
[ angletypes ]<br>
; i j k
func
tHC cth<br>
OM S OM 1 109.500 500.080<br>
OM S OS 1 109.500 500.080<br>
S OS C2 1 120.000 397.480<br>
OS C2 C2 1 107.900 460.240<br>
C2 C2 C2 1 111.000 460.240<br>
C2 C2 C3 1 111.000 460.240<br>
HC C2 HC 1 109.500 292.880<br>
C2 C2 HC 1 109.500 292.880<br>
C3 C2 HC 1 109.500 292.880<br>
C2 C3 HC 1 109.500 292.880<br>
OS C2 HC 1 109.500 292.880<br>
HC C3 HC 1 109.500 292.880<br>
<br>
[ dihedraltypes ]<br>
; i l
func
q0 cq<br>
S OS
1 0.000
3.766 3<br>
OS C2
1 0.000
3.766 3<br>
C2 C2
1 0.000
5.858 3<br>
C2 C3
1 0.000
5.858 3<br>
<br>
<br>
[ dihedraltypes ]<br>
C2 C2 3 9.2789 12.156 -13.120 -3.0597 26.240 -31.495<br>
<br>
<br>
<br>
<br>
<br>
; Include various molecular topologies<br>
#include "1unk.itp"<br>
#include "spc.itp"<br>
#include "1sds.itp"<br>
<br>
[ system ]<br>
; Name<br>
unk in water<br>
<br>
[ molecules ]<br>
; Compound #mols<br>
unk 1<br>
Na 16<br>
SOL 2148<br>
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