# Ligand LINCS error Help **URL:** \ **Category:** User discussions\ **Created:** [October 7, 2022, 1:23am UTC](https://gromacs.bioexcel.eu/t/ligand-lincs-error-help/4975 "2022-10-07T01:23:10Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![mike](https://avatars.discourse-cdn.com/v4/letter/m/58f4c7/32.png) [@mike](https://gromacs.bioexcel.eu/u/mike)\ **Post date:** [October 7, 2022, 1:23am UTC](https://gromacs.bioexcel.eu/t/ligand-lincs-error-help/4975/1 "2022-10-07T01:23:10Z")
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 ---
**Author:** ![alevilla](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/alevilla/32/439_2.png) [@alevilla](https://gromacs.bioexcel.eu/u/alevilla)\ **Post date:** [October 18, 2022, 4:01pm UTC](https://gromacs.bioexcel.eu/t/ligand-lincs-error-help/4975/2 "2022-10-18T16:01:22Z")
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