Ligand LINCS error Help

User discussions
1

GROMACS version: latest
GROMACS modification: Yes
Here post your question

Below are my topology file and a bit of the errors I am receiving.
I have performed a protein-ligand simulation. I received many LINCS errors. When I perform just the protein, the simulation works. Now I tried just doing the ligand, and as suspected, the ligand is giving many LINCS warnings. The LINCS warnings has to do with the angles, how do I fix it? The Lincs warnings are the following:

Step 215, time 0.43 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.848962, max 2.546885 (between atoms 11 and 10)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
11 10 90.0 0.1103 0.3352 0.0945
11 10 90.0 0.1103 0.3352 0.0945
11 10 90.0 0.1103 0.3352 0.0945
11 10 90.0 0.1103 0.3352 0.0945
Wrote pdb files with previous and current coordinates

Step 216, time 0.432 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.075398, max 0.226194 (between atoms 11 and 10)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
11 10 90.0 0.3352 0.1159 0.0945
11 10 90.0 0.3352 0.1159 0.0945
11 10 90.0 0.3352 0.1159 0.0945
11 10 90.0 0.3352 0.1159 0.0945

Step 217, time 0.434 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.849561, max 2.548684 (between atoms 11 and 10)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
11 10 90.0 0.1159 0.3354 0.0945
11 10 90.0 0.1159 0.3354 0.0945
11 10 90.0 0.1159 0.3354 0.0945
11 10 90.0 0.1159 0.3354 0.0945
Wrote pdb files with previous and current coordinates

Step 218, time 0.436 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.080784, max 0.242351 (between atoms 11 and 10)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
11 10 90.0 0.3354 0.1174 0.0945
11 10 90.0 0.3354 0.1174 0.0945
11 10 90.0 0.3354 0.1174 0.0945
11 10 90.0 0.3354 0.1174 0.0945

Step 219, time 0.438 (ps) LINCS WARNING
relative constraint deviation after LINCS:
rms 0.859736, max 2.579207 (between atoms 11 and 10)
bonds that rotated more than 30 degrees:
atom 1 atom 2 angle previous, current, constraint length
6 5 41.8 0.0945 0.0945 0.0945
6 5 41.8 0.0945 0.0945 0.0945
6 5 41.8 0.0945 0.0945 0.0945
6 5 41.8 0.0945 0.0945 0.0945
11 10 90.0 0.1174 0.3382 0.0945
11 10 90.0 0.1174 0.3382 0.0945
11 10 90.0 0.1174 0.3382 0.0945
11 10 90.0 0.1174 0.3382 0.0945
16 15 30.3 0.0945 0.0945 0.0945
16 15 30.3 0.0945 0.0945 0.0945
16 15 30.3 0.0945 0.0945 0.0945
16 15 30.3 0.0945 0.0945 0.0945

Here below is my topolgy file

;
; GENERATED BY LigParGen Server
; Jorgensen Lab @ Yale University
;
[ atomtypes ]
opls_808 O808 15.9990 0.000 A 2.96000E-01 8.78640E-01
opls_823 N823 14.0070 0.000 A 3.25000E-01 7.11280E-01
opls_825 N825 14.0070 0.000 A 3.25000E-01 7.11280E-01
opls_832 H832 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_806 O806 15.9990 0.000 A 2.90000E-01 5.85760E-01
opls_840 H840 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_828 C828 12.0110 0.000 A 3.50000E-01 3.34720E-01
opls_815 H815 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_812 P812 30.9738 0.000 A 3.74000E-01 8.36800E-01
opls_824 C824 12.0110 0.000 A 3.30000E-01 2.76144E-01
opls_834 N834 14.0070 0.000 A 3.25000E-01 7.11280E-01
opls_814 O814 15.9990 0.000 A 3.12000E-01 7.11280E-01
opls_818 C818 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_821 C821 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_829 O829 15.9990 0.000 A 2.96000E-01 8.78640E-01
opls_819 O819 15.9990 0.000 A 2.90000E-01 5.85760E-01
opls_827 C827 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_801 O801 15.9990 0.000 A 2.96000E-01 8.78640E-01
opls_800 P800 30.9738 0.000 A 3.74000E-01 8.36800E-01
opls_831 C831 12.0110 0.000 A 3.55000E-01 3.17984E-01
opls_817 C817 12.0110 0.000 A 3.30000E-01 2.76144E-01
opls_837 O837 15.9990 0.000 A 3.12000E-01 7.11280E-01
opls_839 O839 15.9990 0.000 A 3.12000E-01 7.11280E-01
opls_833 N833 14.0070 0.000 A 3.25000E-01 7.11280E-01
opls_835 H835 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_816 O816 15.9990 0.000 A 2.90000E-01 5.85760E-01
opls_836 H836 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_803 H803 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_813 O813 15.9990 0.000 A 2.96000E-01 8.78640E-01
opls_804 O804 15.9990 0.000 A 3.12000E-01 7.11280E-01
opls_810 H810 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_807 P807 30.9738 0.000 A 3.74000E-01 8.36800E-01
opls_826 C826 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_830 N830 14.0070 0.000 A 3.25000E-01 7.11280E-01
opls_811 O811 15.9990 0.000 A 2.90000E-01 5.85760E-01
opls_805 H805 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_820 C820 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_822 C822 12.0110 0.000 A 3.55000E-01 2.92880E-01
opls_802 O802 15.9990 0.000 A 3.12000E-01 7.11280E-01
opls_838 H838 1.0080 0.000 A 0.00000E+00 0.00000E+00
opls_809 O809 15.9990 0.000 A 3.12000E-01 7.11280E-01
[ moleculetype ]
; Name nrexcl
GTP 3
[ atoms ]
; nr type resnr residue atom cgnr charge mass
1 opls_800 1 GTP P00 1 2.6917 30.9738
2 opls_801 1 GTP O01 1 -1.0843 15.9990
3 opls_802 1 GTP O02 1 -0.9317 15.9990
4 opls_803 1 GTP H03 1 0.4401 1.0080
5 opls_804 1 GTP O04 1 -0.9164 15.9990
6 opls_805 1 GTP H05 1 0.4233 1.0080
7 opls_806 1 GTP O06 1 -1.2431 15.9990
8 opls_807 1 GTP P07 1 2.7415 30.9738
9 opls_808 1 GTP O08 1 -1.0672 15.9990
10 opls_809 1 GTP O09 1 -0.8893 15.9990
11 opls_810 1 GTP H0A 1 0.4202 1.0080
12 opls_811 1 GTP O0B 1 -1.1679 15.9990
13 opls_812 1 GTP P0C 1 2.7075 30.9738
14 opls_813 1 GTP O0D 1 -1.0502 15.9990
15 opls_814 1 GTP O0E 1 -0.9044 15.9990
16 opls_815 1 GTP H0F 1 0.4252 1.0080
17 opls_816 1 GTP O0G 1 -0.8231 15.9990
18 opls_817 1 GTP C0H 1 0.4870 12.0110
19 opls_818 1 GTP C0I 1 -0.0773 12.0110
20 opls_819 1 GTP O0J 1 -0.2361 15.9990
21 opls_820 1 GTP C0K 1 0.1904 12.0110
22 opls_821 1 GTP C0M 1 0.1719 12.0110
23 opls_822 1 GTP C0N 1 0.1224 12.0110
24 opls_823 1 GTP N0O 1 -0.4746 14.0070
25 opls_824 1 GTP C0P 1 0.3162 12.0110
26 opls_825 1 GTP N0Q 1 -0.0612 14.0070
27 opls_826 1 GTP C0R 1 -0.0422 12.0110
28 opls_827 1 GTP C0S 1 0.5194 12.0110
29 opls_828 1 GTP C0T 1 0.4328 12.0110
30 opls_829 1 GTP O0U 1 -0.1798 15.9990
31 opls_830 1 GTP N0V 1 -0.8079 14.0070
32 opls_831 1 GTP C0W 1 0.7577 12.0110
33 opls_832 1 GTP H0X 2 0.4725 1.0080
34 opls_833 1 GTP N0Y 2 -0.4346 14.0070
35 opls_834 1 GTP N0Z 2 -0.7282 14.0070
36 opls_835 1 GTP H10 2 0.4465 1.0080
37 opls_836 1 GTP H11 2 0.4465 1.0080
38 opls_837 1 GTP O12 2 -0.4651 15.9990
39 opls_838 1 GTP H13 2 0.4065 1.0080
40 opls_839 1 GTP O14 2 -0.4416 15.9990
41 opls_840 1 GTP H15 2 0.4070 1.0080
[ bonds ]
2 1 1 0.1480 439320.000
3 1 1 0.1610 192464.000
4 3 1 0.0945 462750.400
5 1 1 0.1610 192464.000
6 5 1 0.0945 462750.400
7 1 1 0.1610 192464.000
8 7 1 0.1610 192464.000
9 8 1 0.1480 439320.000
10 8 1 0.1610 192464.000
11 10 1 0.0945 462750.400
12 8 1 0.1610 192464.000
13 12 1 0.1610 192464.000
14 13 1 0.1480 439320.000
15 13 1 0.1610 192464.000
16 15 1 0.0945 462750.400
17 13 1 0.1610 192464.000
18 17 1 0.1270 367606.240
19 18 1 0.1451 334720.000
20 19 1 0.1360 284512.000
21 20 1 0.1360 284512.000
22 21 1 0.1367 456892.800
23 19 1 0.1367 456892.800
24 21 1 0.1381 357313.600
25 24 1 0.1310 316486.128
26 25 1 0.1320 312896.256
27 26 1 0.1394 343088.000
28 27 1 0.1490 334720.000
29 24 1 0.1374 364844.800
30 28 1 0.1229 476976.000
31 28 1 0.1388 349782.400
32 31 1 0.1365 374886.400
33 31 1 0.1010 363171.200
34 29 1 0.1354 385764.800
35 32 1 0.1381 357313.600
36 35 1 0.1010 363171.200
37 35 1 0.1010 363171.200
38 22 1 0.1364 376560.000
39 38 1 0.0945 462750.400
40 23 1 0.1364 376560.000
41 40 1 0.0945 462750.400
23 22 1 0.1424 392459.200
29 27 1 0.1404 392459.200
34 32 1 0.1339 404174.400

[ angles ]
; ai aj ak funct c0 c1 c2 c3
2 1 3 1 108.230 836.800
1 3 4 1 108.500 460.240
2 1 5 1 108.230 836.800
1 5 6 1 108.500 460.240
2 1 7 1 108.230 836.800
1 7 8 1 120.500 836.800
7 8 9 1 108.230 836.800
7 8 10 1 102.600 376.560
8 10 11 1 108.500 460.240
7 8 12 1 102.600 376.560
8 12 13 1 120.500 836.800
12 13 14 1 108.230 836.800
12 13 15 1 102.600 376.560
13 15 16 1 108.500 460.240
12 13 17 1 102.600 376.560
13 17 18 1 114.540 581.660
17 18 19 1 180.000 1338.880
18 19 20 1 120.360 513.377
19 20 21 1 106.500 585.760
20 21 22 1 110.600 585.760
18 19 23 1 120.000 585.760
20 21 24 1 120.360 513.377
21 24 25 1 112.400 527.184
24 25 26 1 180.000 1338.880
25 26 27 1 111.360 497.143
26 27 28 1 120.670 475.972
21 24 29 1 109.800 585.760
27 28 30 1 120.400 669.440
27 28 31 1 118.180 584.923
28 31 32 1 121.600 585.760
28 31 33 1 116.800 292.880
24 29 34 1 126.200 585.760
31 32 35 1 118.760 505.678
32 35 36 1 119.800 292.880
32 35 37 1 119.800 292.880
21 22 38 1 120.000 585.760
22 38 39 1 113.000 292.880
19 23 40 1 120.000 585.760
23 40 41 1 113.000 292.880
19 23 22 1 107.300 585.760
36 35 37 1 120.000 292.880
29 34 32 1 112.200 585.760
14 13 17 1 108.230 836.800
22 23 40 1 120.000 585.760
15 13 17 1 102.600 376.560
27 29 34 1 132.400 585.760
5 1 7 1 102.600 376.560
9 8 12 1 108.230 836.800
32 31 33 1 119.200 292.880
26 27 29 1 111.000 585.760
23 22 38 1 120.000 585.760
3 1 5 1 102.600 376.560
25 24 29 1 112.400 527.184
9 8 10 1 108.230 836.800
28 27 29 1 120.000 711.280
14 13 15 1 108.230 836.800
24 29 27 1 108.700 585.760
21 22 23 1 107.300 585.760
31 32 34 1 123.300 585.760
22 21 24 1 107.700 585.760
34 32 35 1 118.760 505.678
10 8 12 1 102.600 376.560
30 28 31 1 120.600 669.440
3 1 7 1 102.600 376.560
20 19 23 1 110.600 585.760

[ dihedrals ]
; IMPROPER DIHEDRAL ANGLES
; ai aj ak al funct c0 c1 c2 c3 c4 c5
23 19 18 20 4 180.000 10.460 2
37 35 32 36 4 180.000 10.460 2
33 31 28 32 4 180.000 10.460 2
35 32 31 34 4 180.000 10.460 2
31 28 27 30 4 180.000 43.932 2
26 27 28 29 4 180.000 10.460 2
34 29 24 27 4 180.000 10.460 2
24 21 20 22 4 180.000 10.460 2
40 23 19 22 4 180.000 10.460 2
38 22 21 23 4 180.000 10.460 2

[ dihedrals ]
; PROPER DIHEDRAL ANGLES
; ai aj ak al funct c0 c1 c2 c3 c4 c5
28 27 29 24 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
28 27 26 25 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
25 24 21 22 3 20.920 0.000 -20.920 -0.000 -0.000 0.000
25 24 21 20 3 8.786 0.000 -8.786 -0.000 -0.000 0.000
18 17 13 14 3 0.000 0.000 0.000 -0.000 -0.000 0.000
18 17 13 15 3 1.176 3.527 0.000 -4.703 -0.000 0.000
18 17 13 12 3 1.176 3.527 0.000 -4.703 -0.000 0.000
29 27 26 25 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
29 24 25 26 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
29 24 21 22 3 20.920 0.000 -20.920 -0.000 -0.000 0.000
29 24 21 20 3 8.786 0.000 -8.786 -0.000 -0.000 0.000
32 31 28 27 3 0.000 0.000 0.000 -0.000 -0.000 0.000
32 31 28 30 3 25.476 0.000 -25.476 -0.000 -0.000 0.000
32 34 29 27 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
32 34 29 24 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
22 23 19 18 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
23 22 21 20 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
22 23 19 20 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
23 19 18 17 3 7.845 -1.569 -6.276 -0.000 -0.000 0.000
22 21 20 19 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
23 19 20 21 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
27 29 24 25 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
27 29 24 21 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
27 26 25 24 3 41.840 0.000 -41.840 -0.000 -0.000 0.000
19 18 17 13 3 12.510 0.000 -12.510 -0.000 -0.000 0.000
21 22 23 19 3 9.079 0.000 -9.079 -0.000 -0.000 0.000
21 20 19 18 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
36 35 32 31 3 20.502 0.000 -20.502 -0.000 -0.000 0.000
37 35 32 31 3 20.502 0.000 -20.502 -0.000 -0.000 0.000
37 35 32 34 3 20.502 0.000 -20.502 -0.000 -0.000 0.000
36 35 32 34 3 20.502 0.000 -20.502 -0.000 -0.000 0.000
33 31 28 27 3 20.502 0.000 -20.502 -0.000 -0.000 0.000
33 31 28 30 3 20.502 0.000 -20.502 -0.000 -0.000 0.000
41 40 23 22 3 -0.444 3.833 0.728 -4.117 -0.000 0.000
39 38 22 23 3 -0.444 3.833 0.728 -4.117 -0.000 0.000
41 40 23 19 3 -0.444 3.833 0.728 -4.117 -0.000 0.000
39 38 22 21 3 -0.444 3.833 0.728 -4.117 -0.000 0.000
16 15 13 14 3 0.000 0.000 0.000 -0.000 -0.000 0.000
11 10 8 9 3 0.000 0.000 0.000 -0.000 -0.000 0.000
6 5 1 2 3 0.000 0.000 0.000 -0.000 -0.000 0.000
4 3 1 2 3 0.000 0.000 0.000 -0.000 -0.000 0.000
6 5 1 3 3 0.000 0.000 0.000 -0.000 -0.000 0.000
16 15 13 12 3 0.000 0.000 0.000 -0.000 -0.000 0.000
11 10 8 7 3 0.000 0.000 0.000 -0.000 -0.000 0.000
35 32 31 28 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
35 32 31 33 3 20.502 0.000 -20.502 -0.000 -0.000 0.000
35 32 34 29 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
31 28 27 29 3 29.288 0.000 -29.288 -0.000 -0.000 0.000
31 28 27 26 3 9.079 0.000 -9.079 -0.000 -0.000 0.000
31 32 34 29 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
26 25 24 21 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
26 27 29 24 3 9.079 0.000 -9.079 -0.000 -0.000 0.000
34 29 27 28 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
34 29 27 26 3 9.079 0.000 -9.079 -0.000 -0.000 0.000
34 29 24 25 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
34 29 24 21 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
34 32 31 28 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
34 32 31 33 3 20.920 0.000 -20.920 -0.000 -0.000 0.000
24 21 22 23 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
24 21 20 19 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
30 28 27 29 3 29.288 0.000 -29.288 -0.000 -0.000 0.000
30 28 27 26 3 4.184 0.000 -4.184 -0.000 -0.000 0.000
9 8 7 1 3 0.000 0.000 0.000 -0.000 -0.000 0.000
14 13 12 8 3 0.000 0.000 0.000 -0.000 -0.000 0.000
20 19 18 17 3 4.707 1.569 -6.276 -0.000 -0.000 0.000
38 22 23 19 3 9.079 0.000 -9.079 -0.000 -0.000 0.000
40 23 22 21 3 9.079 0.000 -9.079 -0.000 -0.000 0.000
40 23 22 38 3 9.079 0.000 -9.079 -0.000 -0.000 0.000
40 23 19 18 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
38 22 21 24 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
40 23 19 20 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
38 22 21 20 3 30.334 0.000 -30.334 -0.000 -0.000 0.000
5 1 3 4 3 0.000 0.000 0.000 -0.000 -0.000 0.000
10 8 7 1 3 1.176 3.527 0.000 -4.703 -0.000 0.000
15 13 12 8 3 1.176 3.527 0.000 -4.703 -0.000 0.000
7 1 3 4 3 0.000 0.000 0.000 -0.000 -0.000 0.000
7 1 5 6 3 0.000 0.000 0.000 -0.000 -0.000 0.000
17 13 15 16 3 0.000 0.000 0.000 -0.000 -0.000 0.000
12 8 10 11 3 0.000 0.000 0.000 -0.000 -0.000 0.000
12 8 7 1 3 1.176 3.527 0.000 -4.703 -0.000 0.000
17 13 12 8 3 1.176 3.527 0.000 -4.703 -0.000 0.000
8 7 1 2 3 0.000 0.000 0.000 -0.000 -0.000 0.000
13 12 8 9 3 0.000 0.000 0.000 -0.000 -0.000 0.000
13 12 8 10 3 1.176 3.527 0.000 -4.703 -0.000 0.000
8 7 1 3 3 1.176 3.527 0.000 -4.703 -0.000 0.000
8 7 1 5 3 1.176 3.527 0.000 -4.703 -0.000 0.000
13 12 8 7 3 1.176 3.527 0.000 -4.703 -0.000 0.000

[ pairs ]
2 4 1
2 6 1
4 5 1
3 6 1
2 8 1
1 9 1
4 7 1
3 8 1
1 10 1
6 7 1
5 8 1
1 12 1
7 11 1
9 11 1
7 13 1
9 13 1
8 14 1
11 12 1
10 13 1
8 15 1
8 17 1
12 16 1
14 16 1
12 18 1
14 18 1
13 19 1
16 17 1
15 18 1
17 20 1
18 21 1
18 22 1
17 23 1
19 24 1
20 25 1
23 24 1
22 25 1
21 26 1
21 27 1
20 29 1
22 29 1
24 28 1
25 28 1
21 34 1
26 30 1
24 32 1
26 31 1
19 38 1
20 38 1
18 40 1
29 30 1
27 32 1
25 34 1
29 31 1
27 33 1
26 34 1
21 39 1
20 40 1
19 41 1
21 40 1
30 32 1
28 34 1
24 38 1
23 39 1
30 33 1
28 35 1
22 41 1
29 35 1
33 34 1
31 36 1
33 35 1
31 37 1
34 36 1
34 37 1
38 40 1

2

Hi,
As far as I understood you got LINCS error for the protein-ligand complex. Which atom is in position 1 in your gro file? Atom 1 can belong to the protein or to the ligand. This depends in which order you have the system in the gro file.
You could visualize maybe it helps to tackle the problem.
\Alessandra