Topology for opls

User discussions
1

GROMACS version: 2016.4
GROMACS modification: No
Hi. I am doing a Protein-ligand simulation using gromacs 2016.4 and oplsaa ff. To create the itp file for ligand, topolgen and topolbuild both unavailable. I managed to obtain itp from other servers and showed errors such as [ atomtypes ] not found or opls_800 atom type not found. Why is topolgen and topolbuild not available ?

I am to this new version of forum and I don’t know if it is possible to attach the itp file as such here.

;
;
[ atomtypes ]
opls_805 N805 14.0070 0.000 A 3.25000E-01 7.11280E-01
opls_816 C816 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_817 C817 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_834 H834 1.0080 0.000 A 2.42000E-01 1.25520E-01
opls_804 O804 15.9990 0.000 A 2.96000E-01 8.78640E-01
opls_815 C815 12.0110 0.000 A 3.50000E-01 3.34720E-01
opls_833 H833 1.0080 0.000 A 2.42000E-01 1.25520E-01
opls_802 C802 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_829 H829 1.0080 0.000 A 2.42000E-01 1.25520E-01
opls_835 H835 1.0080 0.000 A 2.42000E-01 1.25520E-01
opls_826 H826 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_825 H825 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_818 C818 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_824 H824 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_809 C809 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_814 C814 12.0110 0.000 A 3.50000E-01 3.34720E-01
opls_819 C819 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_810 C810 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_800 C800 12.0110 0.000 A 3.50000E-01 2.76144E-01
opls_823 H823 1.0080 0.000 A 2.50000E-01 1.25520E-01
opls_806 C806 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_820 S820 32.0600 0.000 A 3.55000E-01 1.04600E+00
opls_827 H827 1.0080 0.000 A 2.42000E-01 1.25520E-01
opls_811 C811 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_812 C812 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_807 N807 14.0070 0.000 A 3.25000E-01 7.11280E-01
opls_822 O822 15.9990 0.000 A 2.96000E-01 7.11280E-01
opls_828 H828 1.0080 0.000 A 2.42000E-01 1.25520E-01
opls_813 O813 15.9990 0.000 A 3.12000E-01 7.11280E-01
opls_803 C803 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_832 H832 1.0080 0.000 A 2.42000E-01 1.25520E-01
opls_801 N801 14.0070 0.000 A 3.25000E-01 7.11280E-01
opls_821 O821 15.9990 0.000 A 2.96000E-01 7.11280E-01
opls_831 H831 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_808 C808 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_830 H830 1.0080 0.000 A 2.42000E-01 1.25520E-01
[ moleculetype ]
; Name nrexcl
UNK 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_800 1 UNK C00 1 0.2166 12.0110
2 opls_801 1 UNK N01 1 -1.4475 14.0070
3 opls_802 1 UNK C02 1 0.2483 12.0110
4 opls_803 1 UNK C03 1 0.6444 12.0110
5 opls_804 1 UNK O04 1 -0.4583 15.9990
6 opls_805 1 UNK N05 1 -0.8730 14.0070
7 opls_806 1 UNK C06 1 0.3716 12.0110
8 opls_807 1 UNK N07 1 -0.4548 14.0070
9 opls_808 1 UNK C08 1 0.0709 12.0110
10 opls_809 1 UNK C09 1 -0.2205 12.0110
11 opls_810 1 UNK C0A 1 -0.0711 12.0110
12 opls_811 1 UNK C0B 1 -0.1939 12.0110
13 opls_812 1 UNK C0C 1 0.1469 12.0110
14 opls_813 1 UNK O0D 1 -0.5007 15.9990
15 opls_814 1 UNK C0E 1 0.0601 12.0110
16 opls_815 1 UNK C0F 1 -0.4773 12.0110
17 opls_816 1 UNK C0G 1 -0.0235 12.0110
18 opls_817 1 UNK C0H 1 -0.1442 12.0110
19 opls_818 1 UNK C0I 1 -0.0953 12.0110
20 opls_819 1 UNK C0J 1 -0.1126 12.0110
21 opls_820 1 UNK S0K 1 1.6129 32.0600
22 opls_821 1 UNK O0M 1 -0.5109 15.9990
23 opls_822 1 UNK O0N 1 -0.5109 15.9990
24 opls_823 1 UNK H0O 1 0.1202 1.0080
25 opls_824 1 UNK H0P 1 0.1202 1.0080
26 opls_825 1 UNK H0Q 1 0.1202 1.0080
27 opls_826 1 UNK H0R 1 0.5068 1.0080
28 opls_827 1 UNK H0S 1 0.1848 1.0080
29 opls_828 1 UNK H0T 1 0.1705 1.0080
30 opls_829 1 UNK H0U 1 0.1650 1.0080
31 opls_830 1 UNK H0V 1 0.1874 1.0080
32 opls_831 1 UNK H0W 1 0.4682 1.0080
33 opls_832 1 UNK H0X 2 0.1735 1.0080
34 opls_833 1 UNK H0Y 2 0.1645 1.0080
35 opls_834 1 UNK H0Z 2 0.1619 1.0080
36 opls_835 1 UNK H10 2 0.1794 1.0080
[ bonds ]
2 1 1 0.1475 282001.600
3 2 1 0.1365 374886.400
4 3 1 0.1444 343088.000
5 4 1 0.1229 476976.000
6 4 1 0.1335 410032.000
7 6 1 0.1381 357313.600
8 7 1 0.1339 404174.400
9 8 1 0.1339 404174.400
10 9 1 0.1400 392459.200
11 10 1 0.1400 392459.200
12 7 1 0.1400 392459.200
13 3 1 0.1340 459403.200
14 13 1 0.1370 376560.000
15 13 1 0.1433 357313.600
16 15 1 0.1370 435136.000
17 16 1 0.1404 392459.200
18 17 1 0.1400 392459.200
19 18 1 0.1400 392459.200
20 15 1 0.1404 392459.200
21 2 1 0.1700 214086.912
22 21 1 0.1440 585760.000
23 21 1 0.1440 585760.000
24 1 1 0.1090 284512.000
25 1 1 0.1090 284512.000
26 1 1 0.1090 284512.000
27 6 1 0.1010 363171.200
28 9 1 0.1080 307105.600
29 10 1 0.1080 307105.600
30 11 1 0.1080 307105.600
31 12 1 0.1080 307105.600
32 14 1 0.0945 462750.400
33 17 1 0.1080 307105.600
34 18 1 0.1080 307105.600
35 19 1 0.1080 307105.600
36 20 1 0.1080 307105.600
12 11 1 0.1400 392459.200
21 16 1 0.1770 284512.000
20 19 1 0.1400 392459.200

[ angles ]
; ai aj ak funct c0 c1 c2 c3
1 2 3 1 112.400 527.184
2 3 4 1 118.760 505.678
3 4 5 1 125.300 669.440
3 4 6 1 115.500 585.760
4 6 7 1 121.900 418.400
6 7 8 1 118.990 539.820
7 8 9 1 117.000 585.760
8 9 10 1 124.000 585.760
9 10 11 1 120.000 527.184
6 7 12 1 120.000 585.760
2 3 13 1 121.200 585.760
3 13 14 1 123.000 585.760
3 13 15 1 117.000 711.280
13 15 16 1 124.000 585.760
15 16 17 1 117.300 711.280
16 17 18 1 120.000 527.184
17 18 19 1 120.000 527.184
13 15 20 1 124.000 585.760
1 2 21 1 112.400 527.184
2 21 22 1 104.360 658.311
2 21 23 1 104.360 658.311
2 1 24 1 109.500 292.880
2 1 25 1 109.500 292.880
2 1 26 1 109.500 292.880
4 6 27 1 119.800 292.880
8 9 28 1 116.000 292.880
9 10 29 1 120.000 292.880
10 11 30 1 120.000 292.880
7 12 31 1 120.000 292.880
13 14 32 1 109.000 292.880
16 17 33 1 120.000 292.880
17 18 34 1 120.000 292.880
18 19 35 1 120.000 292.880
15 20 36 1 120.000 292.880
16 15 20 1 117.300 711.280
5 4 6 1 122.900 669.440
15 16 21 1 111.000 585.760
7 12 11 1 120.000 527.184
10 9 28 1 120.000 292.880
3 2 21 1 112.400 527.184
22 21 23 1 119.000 870.272
19 20 36 1 120.000 292.880
8 7 12 1 124.000 585.760
11 10 29 1 120.000 292.880
19 18 34 1 120.000 292.880
17 16 21 1 119.400 711.280
14 13 15 1 115.690 382.752
12 11 30 1 120.000 292.880
11 12 31 1 120.000 292.880
16 21 23 1 107.200 619.232
7 6 27 1 119.800 292.880
10 11 12 1 120.000 527.184
2 21 16 1 104.360 658.311
24 1 26 1 107.800 276.144
25 1 26 1 107.800 276.144
15 20 19 1 120.000 527.184
4 3 13 1 120.700 711.280
24 1 25 1 107.800 276.144
18 17 33 1 120.000 292.880
20 19 35 1 120.000 292.880
18 19 20 1 120.000 527.184
16 21 22 1 107.200 619.232

[ dihedrals ]
; IMPROPER DIHEDRAL ANGLES
; ai aj ak al funct c0 c1 c2 c3 c4 c5
13 3 2 4 4 180.000 10.460 2
12 7 6 8 4 180.000 10.460 2
20 15 13 16 4 180.000 10.460 2
17 16 21 15 4 180.000 10.460 2
15 13 3 14 4 180.000 10.460 2
27 6 4 7 4 180.000 10.460 2
30 11 10 12 4 180.000 10.460 2
29 10 9 11 4 180.000 10.460 2
35 19 18 20 4 180.000 10.460 2
34 18 17 19 4 180.000 10.460 2
31 12 7 11 4 180.000 10.460 2
36 20 15 19 4 180.000 10.460 2
33 17 16 18 4 180.000 10.460 2
28 9 8 10 4 180.000 10.460 2
6 4 3 5 4 180.000 43.932 2

[ dihedrals ]
; PROPER DIHEDRAL ANGLES
; ai aj ak al funct c0 c1 c2 c3 c4 c5
4 3 2 1 3 1.715 2.845 1.046 -5.607 -0.000 0.000
13 3 4 6 3 4.184 -4.184 0.000 -0.000 -0.000 0.000
13 3 4 5 3 30.334 -5.230 -25.104 -0.000 -0.000 0.000
13 3 2 1 3 5.230 7.322 -12.552 -0.000 -0.000 0.000
20 19 18 17 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
12 11 10 9 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
10 11 12 7 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
18 19 20 15 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
19 18 17 16 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
11 12 7 6 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
11 12 7 8 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
11 10 9 8 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
19 20 15 13 3 29.288 0.000 -29.288 -0.000 -0.000 0.000
19 20 15 16 3 29.288 0.000 -29.288 -0.000 -0.000 0.000
18 17 16 15 3 29.288 0.000 -29.288 -0.000 -0.000 0.000
12 7 6 4 3 8.786 0.000 -8.786 -0.000 -0.000 0.000
12 7 8 9 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
10 9 8 7 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
20 15 13 3 3 16.027 -4.391 -14.029 2.393 -0.000 0.000
20 15 13 14 3 29.288 0.000 -29.288 -0.000 -0.000 0.000
17 16 15 13 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
20 15 16 17 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
17 16 21 2 3 0.006 -4.199 3.213 0.979 -0.000 0.000
7 6 4 3 3 30.288 -4.812 -25.476 -0.000 -0.000 0.000
7 6 4 5 3 25.476 0.000 -25.476 -0.000 -0.000 0.000
9 8 7 6 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
15 13 3 4 3 58.576 0.000 -58.576 -0.000 -0.000 0.000
15 13 3 2 3 58.576 0.000 -58.576 -0.000 -0.000 0.000
16 15 13 3 3 -0.778 -2.335 0.000 3.113 -0.000 0.000
16 15 13 14 3 29.288 0.000 -29.288 -0.000 -0.000 0.000
15 16 21 2 3 0.006 -4.199 3.213 0.979 -0.000 0.000
16 21 2 3 3 -2.897 11.182 12.410 -20.694 -0.000 0.000
16 21 2 1 3 -2.897 11.182 12.410 -20.694 -0.000 0.000
27 6 4 3 3 20.502 0.000 -20.502 -0.000 -0.000 0.000
27 6 4 5 3 20.502 0.000 -20.502 -0.000 -0.000 0.000
27 6 7 12 3 8.786 0.000 -8.786 -0.000 -0.000 0.000
27 6 7 8 3 8.494 0.000 -8.494 -0.000 -0.000 0.000
36 20 19 18 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
33 17 18 19 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
30 11 12 7 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
29 10 11 12 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
35 19 18 17 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
30 11 10 9 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
31 12 11 10 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
34 18 19 20 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
28 9 10 11 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
35 19 20 15 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
34 18 17 16 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
35 19 18 34 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
29 10 9 28 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
31 12 11 30 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
30 11 10 29 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
36 20 19 35 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
34 18 17 33 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
31 12 7 6 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
29 10 9 8 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
31 12 7 8 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
36 20 15 13 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
33 17 16 15 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
36 20 15 16 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
33 17 16 21 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
28 9 8 7 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
26 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000
25 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000
24 1 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000
26 1 2 21 3 -2.935 -1.914 6.096 -1.247 -0.000 0.000
25 1 2 21 3 -2.935 -1.914 6.096 -1.247 -0.000 0.000
24 1 2 21 3 -2.935 -1.914 6.096 -1.247 -0.000 0.000
32 14 13 15 3 -0.444 3.833 0.728 -4.117 -0.000 0.000
32 14 13 3 3 7.037 0.000 -7.037 -0.000 -0.000 0.000
6 4 3 2 3 12.219 6.123 -5.113 -13.230 -0.000 0.000
8 7 6 4 3 9.079 0.000 -9.079 -0.000 -0.000 0.000
5 4 3 2 3 0.000 0.000 0.000 -0.000 -0.000 0.000
14 13 3 4 3 -5.858 -6.694 12.552 -0.000 -0.000 0.000
14 13 3 2 3 58.576 0.000 -58.576 -0.000 -0.000 0.000
22 21 16 17 3 0.000 0.000 0.000 -0.000 -0.000 0.000
23 21 16 17 3 0.000 0.000 0.000 -0.000 -0.000 0.000
23 21 16 15 3 0.000 0.000 0.000 -0.000 -0.000 0.000
22 21 16 15 3 0.000 0.000 0.000 -0.000 -0.000 0.000
22 21 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000
23 21 2 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000
23 21 2 1 3 0.000 0.000 0.000 -0.000 -0.000 0.000
22 21 2 1 3 0.000 0.000 0.000 -0.000 -0.000 0.000
21 16 17 18 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
21 16 15 13 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
21 16 15 20 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
21 2 3 4 3 -3.431 -3.008 10.598 -4.159 -0.000 0.000
21 2 3 13 3 -3.431 -3.008 10.598 -4.159 -0.000 0.000

[ pairs ]
1 4 1
2 5 1
2 6 1
3 7 1
5 7 1
4 8 1
1 13 1
6 9 1
4 12 1
2 14 1
7 10 1
6 11 1
2 15 1
1 16 1
5 13 1
4 14 1
8 11 1
6 13 1
4 15 1
3 16 1
2 17 1
9 12 1
3 20 1
1 22 1
1 23 1
4 21 1
3 22 1
3 23 1
3 24 1
3 25 1
3 26 1
14 16 1
13 17 1
3 27 1
13 19 1
5 27 1
15 18 1
14 20 1
13 21 1
16 19 1
8 27 1
7 28 1
3 32 1
17 20 1
15 22 1
8 29 1
7 30 1
6 31 1
15 23 1
18 21 1
17 22 1
12 27 1
11 28 1
9 30 1
8 31 1
17 23 1
20 21 1
12 29 1
10 31 1
21 24 1
21 25 1
21 26 1
15 32 1
15 33 1
13 36 1
16 34 1
15 35 1
19 33 1
17 35 1
16 36 1
21 33 1
20 34 1
18 36 1
28 29 1
29 30 1
30 31 1
33 34 1
34 35 1
35 36 1

2

I think it’s because you are using an outdated version of gromacs. If you check the top of your appropriate gromacs share folder, you will see that those opls 800 won’t be there. Gromacs 2018 has some of the opls 800 versions

3

Hi. Thanks for the reply.

So there is no other option to create a topology for the gromacs version 2016.4 in opls FF. ?

4

Which server generated that topology? They may have their own force field files you have to download to use the topology. If not, contact the server’s developers and ask for help because they may not realize there are missing parameters.

5

Read this page. Justin provided an answer to a similar question.

https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-users/2018-July/121512.html

6

Hi Justin

Hope this email finds you well.

I have used Ligpargen.

But still I am not sure why the topolgen or topolbuild link isn’t working.

Thank you for the reply Justin.

7

Hi Teslim, that really helps.

Thank you for the effort. I hope I get the answers regarding the topolgen too soon.

8

If LigParGen is generating nonfunctional output, you need to report the issue to their developers. It’s not a GROMACS problem.

TopolGen and topolbuild were added as user contributions on gromacs.org, which appears to have been taken offline. I wrote TopolGen and will tell you it is a boneheaded stupid program that is occasionally useful. LigParGen actually does proper parameter assignment. TopolGen hopes it can match known functional groups. Please get the LigParGen issues sorted out, it will ultimately be less work for you than fixing a topology from TopolGen.

1 Like
9

Thank you. I would definitely sort it out with Ligpargen.

Thanks for the support