On 8/10/2011 12:35 AM, Chunxia Gao wrote:
Dear all,
I generated the molecule topology from antechamber and then coverted to
gromcas topology.
When I tried to use grompp first it gave me this error : there is no such molecule type
SOL, so I checked the topology file and found out there was no #include
"tip3p.itp" . so I added this to the topology file,
so the topology file looked like this:
; oht.top created by rdparm2gmx.pl Thu Oct 6 22:24:42 IST 2011
[ defaults ]
; nbfunc comb-rule gen-pairs fudgeLJ fudgeQQ
1 2 yes 0.5 0.8333
[ atomtypes ]
;name bond_type mass charge ptype sigma epsilon
c3 c3 0.0000 0.0000 A 3.39967e-01 4.57730e-01
h1 h1 0.0000 0.0000 A 2.47135e-01 6.56888e-02
cf cf 0.0000 0.0000 A 3.39967e-01 3.59824e-01
ha ha 0.0000 0.0000 A 2.59964e-01 6.27600e-02
ca ca 0.0000 0.0000 A 3.39967e-01 3.59824e-01
ho ho 0.0000 0.0000 A 0.00000e+00 0.00000e+00
ce ce 0.0000 0.0000 A 3.39967e-01 3.59824e-01
os os 0.0000 0.0000 A 3.00001e-01 7.11280e-01
hc hc 0.0000 0.0000 A 2.64953e-01 6.56888e-02
oh oh 0.0000 0.0000 A 3.06647e-01 8.80314e-01
n3 n3 0.0000 0.0000 A 3.25000e-01 7.11280e-01
[ moleculetype ]
; Name nrexcl
solute 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass typeB
chargeB
1 c3 1 OHT C10 1 -0.08830 12.000000
2 c3 1 OHT C9 2 -0.04620 12.000000
3 ce 1 OHT C8 3 -0.04600 12.000000
4 ca 1 OHT C11 4 -0.05100 12.000000
5 ca 1 OHT C16 5 -0.11090 12.000000
6 ca 1 OHT C15 6 -0.12900 12.000000
7 ca 1 OHT C14 7 -0.12960 12.000000
8 ca 1 OHT C13 8 -0.13230 12.000000
9 ca 1 OHT C12 9 -0.12440 12.000000
10 cf 1 OHT C7 10 0.00410 12.000000
11 ca 1 OHT C1 11 -0.08660 12.000000
12 ca 1 OHT C2 12 -0.07710 12.000000
13 ca 1 OHT C3 13 -0.15850 12.000000
14 ca 1 OHT C4 14 0.12410 12.000000
15 oh 1 OHT O4 15 -0.49780 16.000000
16 ca 1 OHT C5 16 -0.21770 12.000000
17 ca 1 OHT C6 17 -0.08360 12.000000
18 ca 1 OHT C17 18 -0.09110 12.000000
19 ca 1 OHT C18 19 -0.08080 12.000000
20 ca 1 OHT C19 20 -0.16050 12.000000
21 ca 1 OHT C20 21 0.13280 12.000000
22 os 1 OHT O20 22 -0.32490 16.000000
23 c3 1 OHT C23 23 0.12760 12.000000
24 c3 1 OHT C24 24 0.17240 12.000000
25 n3 1 OHT N24 25 -0.74670 14.000000
26 c3 1 OHT C25 26 0.16000 12.000000
27 c3 1 OHT C26 27 0.16650 12.000000
28 ca 1 OHT C21 28 -0.20950 12.000000
29 ca 1 OHT C22 29 -0.07840 12.000000
30 h1 1 OHT H263 30 0.00150 1.000000
31 h1 1 OHT H262 31 0.04950 1.000000
32 h1 1 OHT H261 32 0.04480 1.000000
33 h1 1 OHT H253 33 0.03530 1.000000
34 h1 1 OHT H252 34 0.00500 1.000000
35 h1 1 OHT H251 35 0.05060 1.000000
36 h1 1 OHT H242 36 0.02390 1.000000
37 h1 1 OHT H241 37 0.07020 1.000000
38 h1 1 OHT H232 38 0.05310 1.000000
39 h1 1 OHT H231 39 0.03440 1.000000
40 hc 1 OHT H103 40 0.04260 1.000000
41 hc 1 OHT H102 41 0.03010 1.000000
42 hc 1 OHT H101 42 0.03390 1.000000
43 ho 1 OHT HO4 43 0.41810 1.000000
44 hc 1 OHT H92 44 0.04990 1.000000
45 hc 1 OHT H91 45 0.05550 1.000000
46 ha 1 OHT H6 46 0.13840 1.000000
47 ha 1 OHT H5 47 0.13260 1.000000
48 ha 1 OHT H3 48 0.15160 1.000000
49 ha 1 OHT H22 49 0.13540 1.000000
50 ha 1 OHT H21 50 0.13480 1.000000
51 ha 1 OHT H2 51 0.14400 1.000000
52 ha 1 OHT H19 52 0.14860 1.000000
53 ha 1 OHT H18 53 0.13890 1.000000
54 ha 1 OHT H16 54 0.13590 1.000000
55 ha 1 OHT H15 55 0.13110 1.000000
56 ha 1 OHT H14 56 0.12990 1.000000
57 ha 1 OHT H13 57 0.13140 1.000000
58 ha 1 OHT H12 58 0.13240 1.000000
[ bonds ]
; ai aj funct r k
1 40 1 1.0920e-01 2.8225e+05
1 41 1 1.0920e-01 2.8225e+05
1 42 1 1.0920e-01 2.8225e+05
2 44 1 1.0920e-01 2.8225e+05
2 45 1 1.0920e-01 2.8225e+05
5 54 1 1.0870e-01 2.8811e+05
6 55 1 1.0870e-01 2.8811e+05
7 56 1 1.0870e-01 2.8811e+05
8 57 1 1.0870e-01 2.8811e+05
9 58 1 1.0870e-01 2.8811e+05
12 51 1 1.0870e-01 2.8811e+05
13 48 1 1.0870e-01 2.8811e+05
15 43 1 9.7400e-02 3.0928e+05
16 47 1 1.0870e-01 2.8811e+05
17 46 1 1.0870e-01 2.8811e+05
19 53 1 1.0870e-01 2.8811e+05
20 52 1 1.0870e-01 2.8811e+05
23 38 1 1.0930e-01 2.8108e+05
23 39 1 1.0930e-01 2.8108e+05
24 36 1 1.0930e-01 2.8108e+05
24 37 1 1.0930e-01 2.8108e+05
26 33 1 1.0930e-01 2.8108e+05
26 34 1 1.0930e-01 2.8108e+05
26 35 1 1.0930e-01 2.8108e+05
27 30 1 1.0930e-01 2.8108e+05
27 31 1 1.0930e-01 2.8108e+05
27 32 1 1.0930e-01 2.8108e+05
28 50 1 1.0870e-01 2.8811e+05
29 49 1 1.0870e-01 2.8811e+05
1 2 1 1.5350e-01 2.5363e+05
2 3 1 1.5050e-01 2.7723e+05
3 4 1 1.4720e-01 3.0627e+05
3 10 1 1.3380e-01 4.7062e+05
4 5 1 1.3870e-01 4.0033e+05
4 9 1 1.3870e-01 4.0033e+05
5 6 1 1.3870e-01 4.0033e+05
6 7 1 1.3870e-01 4.0033e+05
7 8 1 1.3870e-01 4.0033e+05
8 9 1 1.3870e-01 4.0033e+05
10 11 1 1.4720e-01 3.0627e+05
10 18 1 1.4720e-01 3.0627e+05
11 12 1 1.3870e-01 4.0033e+05
11 17 1 1.3870e-01 4.0033e+05
12 13 1 1.3870e-01 4.0033e+05
13 14 1 1.3870e-01 4.0033e+05
14 15 1 1.3620e-01 3.2309e+05
14 16 1 1.3870e-01 4.0033e+05
16 17 1 1.3870e-01 4.0033e+05
18 19 1 1.3870e-01 4.0033e+05
18 29 1 1.3870e-01 4.0033e+05
19 20 1 1.3870e-01 4.0033e+05
20 21 1 1.3870e-01 4.0033e+05
21 22 1 1.3730e-01 3.1162e+05
21 28 1 1.3870e-01 4.0033e+05
22 23 1 1.4390e-01 2.5230e+05
23 24 1 1.5350e-01 2.5363e+05
24 25 1 1.4700e-01 2.6828e+05
25 26 1 1.4700e-01 2.6828e+05
25 27 1 1.4700e-01 2.6828e+05
28 29 1 1.3870e-01 4.0033e+05
[ pairs ]
; ai aj funct
40 3 1
41 3 1
42 3 1
3 54 1
3 58 1
4 44 1
4 45 1
4 55 1
4 57 1
5 58 1
5 56 1
6 57 1
7 54 1
7 58 1
8 55 1
9 54 1
9 56 1
10 44 1
10 45 1
10 51 1
10 46 1
10 53 1
10 49 1
11 48 1
11 47 1
12 46 1
13 43 1
13 47 1
14 51 1
14 46 1
15 48 1
15 47 1
16 48 1
16 43 1
17 51 1
18 52 1
18 50 1
19 49 1
20 50 1
21 53 1
21 38 1
21 39 1
21 49 1
22 52 1
22 50 1
22 36 1
22 37 1
24 33 1
24 34 1
24 35 1
24 30 1
24 31 1
24 32 1
25 38 1
25 39 1
26 36 1
26 37 1
26 30 1
26 31 1
26 32 1
27 36 1
27 37 1
27 33 1
27 34 1
27 35 1
28 52 1
29 53 1
36 38 1
36 39 1
37 38 1
37 39 1
40 44 1
40 45 1
41 44 1
41 45 1
42 44 1
42 45 1
46 47 1
48 51 1
49 50 1
52 53 1
54 55 1
55 56 1
56 57 1
57 58 1
1 4 1
1 10 1
2 5 1
2 9 1
2 11 1
2 18 1
3 6 1
3 8 1
3 12 1
3 17 1
3 19 1
3 29 1
4 11 1
4 18 1
4 7 1
5 10 1
5 8 1
6 9 1
9 10 1
10 13 1
10 16 1
10 20 1
10 28 1
11 19 1
11 29 1
11 14 1
12 18 1
12 16 1
12 15 1
13 17 1
15 17 1
17 18 1
18 21 1
19 28 1
19 22 1
20 29 1
20 23 1
21 24 1
22 29 1
22 25 1
23 28 1
23 26 1
23 27 1
[ angles ]
; ai aj ak funct theta cth
1 2 44 1 1.1005e+02 3.8802e+02
1 2 45 1 1.1005e+02 3.8802e+02
2 1 40 1 1.1005e+02 3.8802e+02
2 1 41 1 1.1005e+02 3.8802e+02
2 1 42 1 1.1005e+02 3.8802e+02
3 2 44 1 1.1098e+02 3.9330e+02
3 2 45 1 1.1098e+02 3.9330e+02
4 5 54 1 1.2001e+02 4.0551e+02
4 9 58 1 1.2001e+02 4.0551e+02
5 6 55 1 1.2001e+02 4.0551e+02
6 5 54 1 1.2001e+02 4.0551e+02
6 7 56 1 1.2001e+02 4.0551e+02
7 6 55 1 1.2001e+02 4.0551e+02
7 8 57 1 1.2001e+02 4.0551e+02
8 7 56 1 1.2001e+02 4.0551e+02
8 9 58 1 1.2001e+02 4.0551e+02
9 8 57 1 1.2001e+02 4.0551e+02
11 12 51 1 1.2001e+02 4.0551e+02
11 17 46 1 1.2001e+02 4.0551e+02
12 13 48 1 1.2001e+02 4.0551e+02
13 12 51 1 1.2001e+02 4.0551e+02
14 13 48 1 1.2001e+02 4.0551e+02
14 15 43 1 1.0947e+02 4.0878e+02
14 16 47 1 1.2001e+02 4.0551e+02
16 17 46 1 1.2001e+02 4.0551e+02
17 16 47 1 1.2001e+02 4.0551e+02
18 19 53 1 1.2001e+02 4.0551e+02
18 29 49 1 1.2001e+02 4.0551e+02
19 20 52 1 1.2001e+02 4.0551e+02
20 19 53 1 1.2001e+02 4.0551e+02
21 20 52 1 1.2001e+02 4.0551e+02
21 28 50 1 1.2001e+02 4.0551e+02
22 23 38 1 1.0882e+02 4.2543e+02
22 23 39 1 1.0882e+02 4.2543e+02
23 24 36 1 1.1007e+02 3.8794e+02
23 24 37 1 1.1007e+02 3.8794e+02
24 23 38 1 1.1007e+02 3.8794e+02
24 23 39 1 1.1007e+02 3.8794e+02
25 24 36 1 1.0992e+02 4.1330e+02
25 24 37 1 1.0992e+02 4.1330e+02
25 26 33 1 1.0992e+02 4.1330e+02
25 26 34 1 1.0992e+02 4.1330e+02
25 26 35 1 1.0992e+02 4.1330e+02
25 27 30 1 1.0992e+02 4.1330e+02
25 27 31 1 1.0992e+02 4.1330e+02
25 27 32 1 1.0992e+02 4.1330e+02
28 29 49 1 1.2001e+02 4.0551e+02
29 28 50 1 1.2001e+02 4.0551e+02
30 27 31 1 1.0955e+02 3.2786e+02
30 27 32 1 1.0955e+02 3.2786e+02
31 27 32 1 1.0955e+02 3.2786e+02
33 26 34 1 1.0955e+02 3.2786e+02
33 26 35 1 1.0955e+02 3.2786e+02
34 26 35 1 1.0955e+02 3.2786e+02
36 24 37 1 1.0955e+02 3.2786e+02
38 23 39 1 1.0955e+02 3.2786e+02
40 1 41 1 1.0835e+02 3.2995e+02
40 1 42 1 1.0835e+02 3.2995e+02
41 1 42 1 1.0835e+02 3.2995e+02
44 2 45 1 1.0835e+02 3.2995e+02
1 2 3 1 1.1096e+02 5.3304e+02
2 3 4 1 1.1911e+02 5.2559e+02
2 3 10 1 1.1740e+02 5.4978e+02
3 4 5 1 1.2066e+02 5.4292e+02
3 4 9 1 1.2066e+02 5.4292e+02
3 10 11 1 1.2308e+02 5.4559e+02
3 10 18 1 1.2308e+02 5.4559e+02
4 3 10 1 1.2308e+02 5.4559e+02
4 5 6 1 1.1997e+02 5.6216e+02
4 9 8 1 1.1997e+02 5.6216e+02
5 4 9 1 1.1997e+02 5.6216e+02
5 6 7 1 1.1997e+02 5.6216e+02
6 7 8 1 1.1997e+02 5.6216e+02
7 8 9 1 1.1997e+02 5.6216e+02
10 11 12 1 1.2066e+02 5.4292e+02
10 11 17 1 1.2066e+02 5.4292e+02
10 18 19 1 1.2066e+02 5.4292e+02
10 18 29 1 1.2066e+02 5.4292e+02
11 10 18 1 1.1553e+02 5.3974e+02
11 12 13 1 1.1997e+02 5.6216e+02
11 17 16 1 1.1997e+02 5.6216e+02
12 11 17 1 1.1997e+02 5.6216e+02
12 13 14 1 1.1997e+02 5.6216e+02
13 14 15 1 1.1994e+02 5.8450e+02
13 14 16 1 1.1997e+02 5.6216e+02
14 16 17 1 1.1997e+02 5.6216e+02
15 14 16 1 1.1994e+02 5.8450e+02
18 19 20 1 1.1997e+02 5.6216e+02
18 29 28 1 1.1997e+02 5.6216e+02
19 18 29 1 1.1997e+02 5.6216e+02
19 20 21 1 1.1997e+02 5.6216e+02
20 21 22 1 1.1920e+02 5.8400e+02
20 21 28 1 1.1997e+02 5.6216e+02
21 22 23 1 1.1797e+02 5.2108e+02
21 28 29 1 1.1997e+02 5.6216e+02
22 21 28 1 1.1920e+02 5.8400e+02
22 23 24 1 1.0842e+02 5.6718e+02
23 24 25 1 1.1038e+02 5.5379e+02
24 25 26 1 1.1090e+02 5.3564e+02
24 25 27 1 1.1090e+02 5.3564e+02
26 25 27 1 1.1090e+02 5.3564e+02
[ dihedrals ]
;i j k l func C0 ... C5
40 1 2 3 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000 ;
41 1 2 3 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000 ;
42 1 2 3 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000 ;
3 4 5 54 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
3 4 9 58 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
4 3 2 44 3 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 ;
4 3 2 45 3 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 ;
4 5 6 55 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
4 9 8 57 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
5 4 9 58 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
5 6 7 56 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
6 7 8 57 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
7 6 5 54 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
7 8 9 58 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
8 7 6 55 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
9 4 5 54 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
9 8 7 56 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
10 3 2 44 3 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 ;
10 3 2 45 3 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 ;
10 11 12 51 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
10 11 17 46 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
10 18 19 53 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
10 18 29 49 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
11 12 13 48 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
11 17 16 47 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
12 11 17 46 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
13 14 15 43 3 7.53120 0.00000 -7.53120 0.00000
0.00000 0.00000 ;
13 14 16 47 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
14 13 12 51 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
14 16 17 46 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
15 14 13 48 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
15 14 16 47 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
16 14 13 48 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
16 14 15 43 3 7.53120 0.00000 -7.53120 0.00000
0.00000 0.00000 ;
17 11 12 51 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
18 19 20 52 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
18 29 28 50 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
19 18 29 49 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
20 21 28 50 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
21 20 19 53 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
21 22 23 38 3 1.60247 4.80742 0.00000 -6.40989
0.00000 0.00000 ;
21 22 23 39 3 1.60247 4.80742 0.00000 -6.40989
0.00000 0.00000 ;
21 28 29 49 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
22 21 20 52 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
22 21 28 50 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
22 23 24 36 3 1.04600 -1.04600 0.00000 0.00000
0.00000 0.00000 ;
22 23 24 37 3 1.04600 -1.04600 0.00000 0.00000
0.00000 0.00000 ;
24 25 26 33 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
24 25 26 34 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
24 25 26 35 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
24 25 27 30 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
24 25 27 31 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
24 25 27 32 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
25 24 23 38 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000 ;
25 24 23 39 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000 ;
26 25 24 36 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
26 25 24 37 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
26 25 27 30 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
26 25 27 31 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
26 25 27 32 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
27 25 24 36 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
27 25 24 37 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
27 25 26 33 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
27 25 26 34 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
27 25 26 35 3 1.25520 3.76560 0.00000 -5.02080
0.00000 0.00000 ;
28 21 20 52 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
29 18 19 53 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
36 24 23 38 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000 ;
36 24 23 39 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000 ;
37 24 23 38 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000 ;
37 24 23 39 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000 ;
40 1 2 44 3 0.62760 1.88280 0.00000 -2.51040
0.00000 0.00000 ;
40 1 2 45 3 0.62760 1.88280 0.00000 -2.51040
0.00000 0.00000 ;
41 1 2 44 3 0.62760 1.88280 0.00000 -2.51040
0.00000 0.00000 ;
41 1 2 45 3 0.62760 1.88280 0.00000 -2.51040
0.00000 0.00000 ;
42 1 2 44 3 0.62760 1.88280 0.00000 -2.51040
0.00000 0.00000 ;
42 1 2 45 3 0.62760 1.88280 0.00000 -2.51040
0.00000 0.00000 ;
46 17 16 47 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
48 13 12 51 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
49 29 28 50 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
52 20 19 53 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
54 5 6 55 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
55 6 7 56 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
56 7 8 57 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
57 8 9 58 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
4 6 5 54 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
5 7 6 55 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
6 8 7 56 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
7 9 8 57 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
4 8 9 58 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
11 13 12 51 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
12 14 13 48 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
14 17 16 47 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
11 16 17 46 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
18 20 19 53 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
19 21 20 52 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
21 29 28 50 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
18 28 29 49 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
1 2 3 4 3 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 ;
1 2 3 10 3 0.00000 0.00000 0.00000 0.00000
0.00000 0.00000 ;
2 3 4 5 3 21.33840 0.00000 -21.33840 0.00000
0.00000 0.00000 ;
2 3 4 9 3 21.33840 0.00000 -21.33840 0.00000
0.00000 0.00000 ;
2 3 10 11 3 55.64720 0.00000 -55.64720 0.00000
0.00000 0.00000 ;
2 3 10 18 3 55.64720 0.00000 -55.64720 0.00000
0.00000 0.00000 ;
3 4 5 6 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
3 4 9 8 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
3 10 11 12 3 21.33840 0.00000 -21.33840 0.00000
0.00000 0.00000 ;
3 10 11 17 3 21.33840 0.00000 -21.33840 0.00000
0.00000 0.00000 ;
3 10 18 19 3 21.33840 0.00000 -21.33840 0.00000
0.00000 0.00000 ;
3 10 18 29 3 21.33840 0.00000 -21.33840 0.00000
0.00000 0.00000 ;
4 3 10 11 3 55.64720 0.00000 -55.64720 0.00000
0.00000 0.00000 ;
4 3 10 18 3 55.64720 0.00000 -55.64720 0.00000
0.00000 0.00000 ;
4 5 6 7 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
4 9 8 7 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
5 4 3 10 3 55.64720 0.00000 -55.64720 0.00000
0.00000 0.00000 ;
5 4 9 8 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
5 6 7 8 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
6 5 4 9 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
6 7 8 9 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
9 4 3 10 3 55.64720 0.00000 -55.64720 0.00000
0.00000 0.00000 ;
10 11 12 13 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
10 11 17 16 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
10 18 19 20 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
10 18 29 28 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
11 10 18 19 3 21.33840 0.00000 -21.33840 0.00000
0.00000 0.00000 ;
11 10 18 29 3 21.33840 0.00000 -21.33840 0.00000
0.00000 0.00000 ;
11 12 13 14 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
11 17 16 14 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
12 11 10 18 3 21.33840 0.00000 -21.33840 0.00000
0.00000 0.00000 ;
12 11 17 16 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
12 13 14 15 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
12 13 14 16 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
13 12 11 17 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
13 14 16 17 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
15 14 16 17 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
17 11 10 18 3 21.33840 0.00000 -21.33840 0.00000
0.00000 0.00000 ;
18 19 20 21 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
18 29 28 21 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
19 18 29 28 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
19 20 21 22 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
19 20 21 28 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
20 19 18 29 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
20 21 22 23 3 7.53120 0.00000 -7.53120 0.00000
0.00000 0.00000 ;
20 21 28 29 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
21 22 23 24 3 1.60247 4.80742 0.00000 -6.40989
0.00000 0.00000 ;
22 21 28 29 3 30.33400 0.00000 -30.33400 0.00000
0.00000 0.00000 ;
22 23 24 25 3 0.65270 1.95811 0.00000 -2.61082
0.00000 0.00000 ;
23 22 21 28 3 7.53120 0.00000 -7.53120 0.00000
0.00000 0.00000 ;
23 24 25 26 3 5.27184 3.76560 -4.01664 -5.02080
0.00000 0.00000 ;
23 24 25 27 3 5.27184 3.76560 -4.01664 -5.02080
0.00000 0.00000 ;
2 4 3 10 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
5 9 4 3 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
11 18 10 3 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
12 17 11 10 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
13 16 14 15 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
19 29 18 10 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
20 28 21 22 3 9.20480 0.00000 -9.20480 0.00000
0.00000 0.00000 ;
; water topology
#include "tip3p.itp"
grompp is not detecting the change of [moleculetype], so you will have
to look at the contents of that tip3p.itp and see why. I think you will
need to #include some standard force field to get the water parameters.
Put the #include for tip3p.itp above your [moleculetype] to get some
different diagnostics that may be more helpful.
Mark
[ system ]
58 system in water
[ molecules ]
; Compound nmols
solute 1
SOL 1339
and this time it gave me another wrong message: [ file tip3p.itp, line 52 ]:
Atom index (1) in settles out of bounds (1-0).
This probably means that you have inserted topology section "settles"
in a part belonging to a different molecule than you intended to.
In that case move the "settles" section to the right molecule.
I cannot figure out why, does anyone have any idea about this?
Regards
Chunxia
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