creating topolgy for small organic molecule in complex with a protein with unnatural residue

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1

GROMACS version:gromacs 2018
GROMACS modification: no
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Dear GROMACS users.

I am trying to run md simulation on a complex composed of a protein with an unnatural residue (FGL) and a small organic molecule (SGC). I had to use CHARMM27.ff because of formylglycine (FGL) residue in protein. So I obtained all the required topology and parameter files from https://www.swisssidechain.ch/MD/gromacs.php server to run MD simulation on the free protein and then used https://www.swissparam.ch/ to get the topology and parameter files compatible with charmm27.ff for the small organic molecule. I simply performed MD simulations on the protein without any problem. But now, when I want to create the topology for the small molecule, I face some problems. All of I have done about creating small molecule topology step by step is:
separate small organic molecule (SGC) from the complex and save in .pdb file
convert the SGC.pdb file to SGC.mol2 file with all of hydrogens using discover studio visulizer.
used “perl sort_mol2_bonds.pl SGC.mol2 SGC_fix.mol2” to correct any strange bond order
upload SGC_fix.mol2 in https://www.swissparam.ch/
topology and parameters file I obtained are:
SGC_fix.mol2, SGC_fix.par, SGC_fix.pdb, SGC_fix.psf, SGC_fix.rtf, SGC_fix.crd and SGC_fix.itp

according to protein-ligand complex GROMACS tutorial , I created topology and coordinate files for the protein, then inserted a line #include "SGC_fix.itp" into topol.top after the position restraint file . But I didnt know which one of these files should I add at the top of topology . so I reffered to https://www.swissparam.ch/SwissParam_gromacs_tutorial.html to know how should I modifiy the topolgy file . So added "#include “SGC_fix.itp” right after ; Include forcefield parameters
#include “charmm27.ff/forcefield.itp” and before [moleculetype] section. Then, in the [molecules] section, right after lines indicating the number of protein, added the following line :
ligand 1

After that, merged the protein.gro and the SGC.gro files in a complex.gro file and modified the number of atoms in the second line of the coordinate file.
defined the unit cell and filled it with water
There was no problem till now. but when I want to addd ions to the system and issued the comaand:
gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
I get some warnings:

NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.

Setting the LD random seed to 1794072544

WARNING 1 [file SGC_fix.itp, line 11]:
Overriding atomtype C=C

WARNING 2 [file SGC_fix.itp, line 17]:
Overriding atomtype SO2

Generated 28441 of the 28441 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 25311 of the 28441 1-4 parameter combinations

2

Hi,
the warnings tell that atomtype C=C and SO2 are defined more than one time in the directive [ atomtype ] and that the values in SGC_fix.itp is used (since I guess it is the last one in order)
I suggest you check the [atomtype] directive in your force field file to understand what is going on and if possible avoid to define the atomtype more than once.
Best regards
Alessandra

3

Dear Dr. Avilla

Thank you for replying

I checked my topology file in terms of overriding atomtypes, but could not find any strange thing in that. I send my topology file and would be grateful if you see it to check if there is something wrong in it?

With best regards
Farial

the warnings I got were:

WARNING 1 [file SGC_fix.itp, line 11]:
Overriding atomtype C=C

WARNING 2 [file SGC_fix.itp, line 17]:
Overriding atomtype SO2

; ----
; Built itp for WTSGC.mol2
; by user vzoete Sat Oct 16 09:02:46 UTC 2021
; ----
;

[ atomtypes ]
; name at.num mass charge ptype sigma epsilon
CR 6 12.0110 0.0 A 0.387541 0.230120
OR 8 15.9994 0.0 A 0.315378 0.636386
C=C 6 12.0110 0.0 A 0.372396 0.284512
HOR 1 1.0079 0.0 A 0.040001 0.192464
NC=O 7 14.0067 0.0 A 0.329632 0.836800
C=O 6 12.0110 0.0 A 0.356359 0.460240
O=C 8 15.9994 0.0 A 0.302905 0.502080
HNCO 1 1.0079 0.0 A 0.040001 0.192464
SO2 16 32.0660 0.0 A 0.374177 1.966480
O2CM 8 15.9994 0.0 A 0.302905 0.502080
HOS 1 1.0079 0.0 A 0.040001 0.192464
HCMM 1 1.0079 0.0 A 0.235197 0.092048

[ pairtypes ]
; i j func sigma1-4 epsilon1-4 ; THESE ARE 1-4 INTERACTIONS
CR CR 1 0.338541 0.041840
CR OR 1 0.326960 0.163176
CR C=C 1 0.355469 0.109105
CR HOR 1 0.189271 0.089737
CR NC=O 1 0.334087 0.187114
CR C=O 1 0.347450 0.138768
CR O=C 1 0.293997 0.144938
CR HNCO 1 0.189271 0.089737
CR SO2 1 0.356359 0.286841
CR O2CM 1 0.320723 0.144938
CR HOS 1 0.189271 0.089737
CR HCMM 1 0.286869 0.062059
O=C OR 1 0.282415 0.565258
O=C C=C 1 0.310924 0.377952
O=C HOR 1 0.144726 0.310857
O=C NC=O 1 0.289542 0.648182
O=C C=O 1 0.302905 0.480705
O=C O=C 1 0.249452 0.502080
O=C HNCO 1 0.144726 0.310857
O=C SO2 1 0.311814 0.993645
O=C O2CM 1 0.276179 0.502080
O=C HOS 1 0.144726 0.310857
O=C HCMM 1 0.242324 0.214978

[ moleculetype ]
; Name nrexcl
WTSGC 3

[ atoms ]
; nr type resnr resid atom cgnr charge mass
1 CR 1 LIG C1 1 0.2800 12.0110
2 OR 1 LIG O2 2 -0.5600 15.9994
3 CR 1 LIG C3 3 0.2800 12.0110
4 CR 1 LIG C4 4 0.5600 12.0110
5 CR 1 LIG C5 5 0.2800 12.0110
6 CR 1 LIG C6 6 0.2800 12.0110
7 OR 1 LIG O16 7 -0.5600 15.9994
8 CR 1 LIG C17 8 0.2800 12.0110
9 CR 1 LIG C18 9 0.3001 12.0110
10 CR 1 LIG C20 10 0.4182 12.0110
11 C=C 1 LIG C21 11 -0.2882 12.0110
12 C=C 1 LIG C23 12 -0.2882 12.0110
13 CR 1 LIG C24 13 0.1382 12.0110
14 OR 1 LIG O22 14 -0.6800 15.9994
15 HOR 1 LIG H42 15 0.4000 1.0079
16 NC=O 1 LIG N19 16 -0.7301 14.0067
17 C=O 1 LIG C47 17 0.5690 12.0110
18 O=C 1 LIG O48 18 -0.5700 15.9994
19 HNCO 1 LIG H52 19 0.3700 1.0079
20 CR 1 LIG C49 20 0.0610 12.0110
21 CR 1 LIG C50 21 0.0000 12.0110
22 CR 1 LIG C51 22 0.0000 12.0110
23 OR 1 LIG O15 23 -0.6800 15.9994
24 HOR 1 LIG H36 24 0.4000 1.0079
25 CR 1 LIG C7 25 0.2800 12.0110
26 OR 1 LIG O8 26 -0.6800 15.9994
27 HOR 1 LIG H32 27 0.4000 1.0079
28 OR 1 LIG O10 28 -0.4637 15.9994
29 SO2 1 LIG S11 29 1.2011 32.0660
30 O2CM 1 LIG O12 30 -0.6500 15.9994
31 OR 1 LIG O13 31 -0.6837 15.9994
32 HOS 1 LIG H34 32 0.5000 1.0079
33 OR 1 LIG O14 33 -0.6837 15.9994
34 HOS 1 LIG H35 34 0.5000 1.0079
35 OR 1 LIG O9 35 -0.6800 15.9994
36 HOR 1 LIG H33 36 0.4000 1.0079
37 HCMM 1 LIG HC 37 0.0000 1.0079
38 HCMM 1 LIG HC1 38 0.0000 1.0079
39 HCMM 1 LIG HC2 39 0.0000 1.0079
40 HCMM 1 LIG HC3 40 0.0000 1.0079
41 HCMM 1 LIG HC4 41 0.0000 1.0079
42 HCMM 1 LIG HC5 42 0.0000 1.0079
43 HCMM 1 LIG HC6 43 0.0000 1.0079
44 HCMM 1 LIG HC7 44 0.0000 1.0079
45 HCMM 1 LIG HC8 45 0.0000 1.0079
46 HCMM 1 LIG HC9 46 0.1500 1.0079
47 HCMM 1 LIG HC10 47 0.1500 1.0079
48 HCMM 1 LIG HC11 48 0.0000 1.0079
49 HCMM 1 LIG HC12 49 0.0000 1.0079
50 HCMM 1 LIG HC13 50 0.0000 1.0079
51 HCMM 1 LIG HC14 51 0.0000 1.0079
52 HCMM 1 LIG HC15 52 0.0000 1.0079
53 HCMM 1 LIG HC16 53 0.0000 1.0079
54 HCMM 1 LIG HC17 54 0.0000 1.0079
55 HCMM 1 LIG HC18 55 0.0000 1.0079
56 HCMM 1 LIG HC19 56 0.0000 1.0079
57 HCMM 1 LIG HC20 57 0.0000 1.0079
58 HCMM 1 LIG HC21 58 0.0000 1.0079
59 HCMM 1 LIG HC22 59 0.0000 1.0079

[ bonds ]
; ai aj fu b0 kb, b0 kb
1 3 1 0.15080 256422.3 0.15080 256422.3
1 25 1 0.15080 256422.3 0.15080 256422.3
1 2 1 0.14180 303937.5 0.14180 303937.5
2 4 1 0.14180 303937.5 0.14180 303937.5
3 35 1 0.14180 303937.5 0.14180 303937.5
3 6 1 0.15080 256422.3 0.15080 256422.3
4 5 1 0.15080 256422.3 0.15080 256422.3
4 7 1 0.14180 303937.5 0.14180 303937.5
5 23 1 0.14180 303937.5 0.14180 303937.5
5 6 1 0.15080 256422.3 0.15080 256422.3
6 28 1 0.14180 303937.5 0.14180 303937.5
7 8 1 0.14180 303937.5 0.14180 303937.5
8 9 1 0.15080 256422.3 0.15080 256422.3
9 10 1 0.15080 256422.3 0.15080 256422.3
9 16 1 0.14360 280872.8 0.14360 280872.8
10 14 1 0.14180 303937.5 0.14180 303937.5
10 11 1 0.14820 273344.9 0.14820 273344.9
11 12 1 0.13330 572403.8 0.13330 572403.8
12 13 1 0.14820 273344.9 0.14820 273344.9
14 15 1 0.09720 469365.3 0.09720 469365.3
16 17 1 0.13690 351030.1 0.13690 351030.1
16 19 1 0.10150 401254.8 0.10150 401254.8
17 18 1 0.12220 779866.6 0.12220 779866.6
17 20 1 0.14920 252327.8 0.14920 252327.8
20 21 1 0.15080 256422.3 0.15080 256422.3
21 22 1 0.15080 256422.3 0.15080 256422.3
23 24 1 0.09720 469365.3 0.09720 469365.3
25 26 1 0.14180 303937.5 0.14180 303937.5
26 27 1 0.09720 469365.3 0.09720 469365.3
28 29 1 0.16300 320738.7 0.16300 320738.7
29 30 1 0.14500 647258.9 0.14500 647258.9
29 33 1 0.16300 320738.7 0.16300 320738.7
29 31 1 0.16300 320738.7 0.16300 320738.7
31 32 1 0.09860 430161.2 0.09860 430161.2
33 34 1 0.09860 430161.2 0.09860 430161.2
35 36 1 0.09720 469365.3 0.09720 469365.3
37 1 1 0.10930 287014.9 0.10930 287014.9
38 3 1 0.10930 287014.9 0.10930 287014.9
39 4 1 0.10930 287014.9 0.10930 287014.9
40 5 1 0.10930 287014.9 0.10930 287014.9
41 6 1 0.10930 287014.9 0.10930 287014.9
42 8 1 0.10930 287014.9 0.10930 287014.9
43 8 1 0.10930 287014.9 0.10930 287014.9
44 9 1 0.10930 287014.9 0.10930 287014.9
45 10 1 0.10930 287014.9 0.10930 287014.9
46 11 1 0.10830 311344.8 0.10830 311344.8
47 12 1 0.10830 311344.8 0.10830 311344.8
48 20 1 0.10930 287014.9 0.10930 287014.9
49 20 1 0.10930 287014.9 0.10930 287014.9
50 21 1 0.10930 287014.9 0.10930 287014.9
51 21 1 0.10930 287014.9 0.10930 287014.9
52 25 1 0.10930 287014.9 0.10930 287014.9
53 25 1 0.10930 287014.9 0.10930 287014.9
54 13 1 0.10930 287014.9 0.10930 287014.9
55 13 1 0.10930 287014.9 0.10930 287014.9
56 13 1 0.10930 287014.9 0.10930 287014.9
57 22 1 0.10930 287014.9 0.10930 287014.9
58 22 1 0.10930 287014.9 0.10930 287014.9
59 22 1 0.10930 287014.9 0.10930 287014.9

[ pairs ]
; ai aj fu
1 5 1
1 7 1
1 39 1
1 28 1
1 41 1
1 36 1
1 27 1
2 6 1
2 35 1
2 38 1
2 26 1
2 52 1
2 53 1
2 23 1
2 40 1
2 8 1
3 4 1
3 26 1
3 52 1
3 53 1
3 23 1
3 40 1
3 29 1
4 25 1
4 37 1
4 28 1
4 41 1
4 24 1
4 9 1
4 42 1
4 43 1
5 8 1
5 35 1
5 38 1
5 29 1
6 25 1
6 37 1
6 36 1
6 7 1
6 39 1
6 24 1
6 30 1
6 31 1
6 33 1
7 23 1
7 40 1
7 10 1
7 16 1
7 44 1
8 39 1
8 11 1
8 14 1
8 45 1
8 17 1
8 19 1
9 12 1
9 46 1
9 15 1
9 18 1
9 20 1
10 42 1
10 43 1
10 17 1
10 19 1
10 13 1
10 47 1
11 16 1
11 44 1
11 15 1
11 54 1
11 55 1
11 56 1
12 14 1
12 45 1
13 46 1
14 16 1
14 44 1
14 46 1
15 45 1
16 42 1
16 43 1
16 45 1
16 21 1
16 48 1
16 49 1
17 44 1
17 22 1
17 50 1
17 51 1
18 19 1
18 21 1
18 48 1
18 49 1
19 44 1
19 20 1
20 57 1
20 58 1
20 59 1
22 48 1
22 49 1
23 39 1
23 28 1
23 41 1
24 40 1
25 35 1
25 38 1
26 37 1
27 52 1
27 53 1
28 35 1
28 38 1
28 40 1
28 32 1
28 34 1
29 41 1
30 32 1
30 34 1
31 34 1
32 33 1
35 37 1
35 41 1
36 38 1
37 38 1
37 52 1
37 53 1
38 41 1
39 40 1
40 41 1
42 44 1
43 44 1
44 45 1
45 46 1
46 47 1
47 54 1
47 55 1
47 56 1
48 50 1
48 51 1
49 50 1
49 51 1
50 57 1
50 58 1
50 59 1
51 57 1
51 58 1
51 59 1

[ angles ]
; ai aj ak fu th0 kth ub0 kub th0 kth ub0 kub
2 1 3 1 108.1330 597.39 108.1330 597.39
2 1 25 1 108.1330 597.39 108.1330 597.39
2 1 37 1 108.5770 470.32 108.5770 470.32
3 1 25 1 109.6080 512.48 109.6080 512.48
3 1 37 1 110.5490 383.00 110.5490 383.00
25 1 37 1 110.5490 383.00 110.5490 383.00
1 2 4 1 106.9260 720.84 106.9260 720.84
1 3 6 1 109.6080 512.48 109.6080 512.48
1 3 35 1 108.1330 597.39 108.1330 597.39
1 3 38 1 110.5490 383.00 110.5490 383.00
6 3 35 1 108.1330 597.39 108.1330 597.39
6 3 38 1 110.5490 383.00 110.5490 383.00
35 3 38 1 108.5770 470.32 108.5770 470.32
2 4 5 1 108.1330 597.39 108.1330 597.39
2 4 7 1 111.3680 696.15 111.3680 696.15
2 4 39 1 108.5770 470.32 108.5770 470.32
5 4 7 1 108.1330 597.39 108.1330 597.39
5 4 39 1 110.5490 383.00 110.5490 383.00
7 4 39 1 108.5770 470.32 108.5770 470.32
4 5 6 1 109.6080 512.48 109.6080 512.48
4 5 23 1 108.1330 597.39 108.1330 597.39
4 5 40 1 110.5490 383.00 110.5490 383.00
6 5 23 1 108.1330 597.39 108.1330 597.39
6 5 40 1 110.5490 383.00 110.5490 383.00
23 5 40 1 108.5770 470.32 108.5770 470.32
3 6 5 1 109.6080 512.48 109.6080 512.48
3 6 28 1 108.1330 597.39 108.1330 597.39
3 6 41 1 110.5490 383.00 110.5490 383.00
5 6 28 1 108.1330 597.39 108.1330 597.39
5 6 41 1 110.5490 383.00 110.5490 383.00
28 6 41 1 108.5770 470.32 108.5770 470.32
4 7 8 1 106.9260 720.84 106.9260 720.84
7 8 9 1 108.1330 597.39 108.1330 597.39
7 8 42 1 108.5770 470.32 108.5770 470.32
7 8 43 1 108.5770 470.32 108.5770 470.32
9 8 42 1 110.5490 383.00 110.5490 383.00
9 8 43 1 110.5490 383.00 110.5490 383.00
42 8 43 1 108.8360 310.74 108.8360 310.74
8 9 10 1 109.6080 512.48 109.6080 512.48
8 9 16 1 109.9600 632.32 109.9600 632.32
8 9 44 1 110.5490 383.00 110.5490 383.00
10 9 16 1 109.9600 632.32 109.9600 632.32
10 9 44 1 110.5490 383.00 110.5490 383.00
16 9 44 1 107.6460 445.64 107.6460 445.64
9 10 11 1 109.4450 443.23 109.4450 443.23
9 10 14 1 108.1330 597.39 108.1330 597.39
9 10 45 1 110.5490 383.00 110.5490 383.00
11 10 14 1 108.6990 646.77 108.6990 646.77
11 10 45 1 110.2920 380.59 110.2920 380.59
14 10 45 1 108.5770 470.32 108.5770 470.32
10 11 12 1 122.1410 404.68 122.1410 404.68
10 11 46 1 120.1080 268.59 120.1080 268.59
12 11 46 1 121.0040 322.18 121.0040 322.18
11 12 13 1 122.1410 404.68 122.1410 404.68
11 12 47 1 121.0040 322.18 121.0040 322.18
13 12 47 1 120.1080 268.59 120.1080 268.59
12 13 54 1 110.2920 380.59 110.2920 380.59
12 13 55 1 110.2920 380.59 110.2920 380.59
12 13 56 1 110.2920 380.59 110.2920 380.59
54 13 55 1 108.8360 310.74 108.8360 310.74
54 13 56 1 108.8360 310.74 108.8360 310.74
55 13 56 1 108.8360 310.74 108.8360 310.74
10 14 15 1 106.5030 477.55 106.5030 477.55
9 16 17 1 119.6000 494.41 119.6000 494.41
9 16 19 1 120.0660 332.42 120.0660 332.42
17 16 19 1 120.2770 346.27 120.2770 346.27
16 17 18 1 127.1520 546.20 127.1520 546.20
16 17 20 1 112.7350 592.57 112.7350 592.57
18 17 20 1 124.4100 564.87 124.4100 564.87
17 20 21 1 107.5170 467.91 107.5170 467.91
17 20 48 1 108.3850 391.44 108.3850 391.44
17 20 49 1 108.3850 391.44 108.3850 391.44
21 20 48 1 110.5490 383.00 110.5490 383.00
21 20 49 1 110.5490 383.00 110.5490 383.00
48 20 49 1 108.8360 310.74 108.8360 310.74
20 21 22 1 109.6080 512.48 109.6080 512.48
20 21 50 1 110.5490 383.00 110.5490 383.00
20 21 51 1 110.5490 383.00 110.5490 383.00
22 21 50 1 110.5490 383.00 110.5490 383.00
22 21 51 1 110.5490 383.00 110.5490 383.00
50 21 51 1 108.8360 310.74 108.8360 310.74
21 22 57 1 110.5490 383.00 110.5490 383.00
21 22 58 1 110.5490 383.00 110.5490 383.00
21 22 59 1 110.5490 383.00 110.5490 383.00
57 22 58 1 108.8360 310.74 108.8360 310.74
57 22 59 1 108.8360 310.74 108.8360 310.74
58 22 59 1 108.8360 310.74 108.8360 310.74
5 23 24 1 106.5030 477.55 106.5030 477.55
1 25 26 1 108.1330 597.39 108.1330 597.39
1 25 52 1 110.5490 383.00 110.5490 383.00
1 25 53 1 110.5490 383.00 110.5490 383.00
26 25 52 1 108.5770 470.32 108.5770 470.32
26 25 53 1 108.5770 470.32 108.5770 470.32
52 25 53 1 108.8360 310.74 108.8360 310.74
25 26 27 1 106.5030 477.55 106.5030 477.55
6 28 29 1 116.3460 825.03 116.3460 825.03
28 29 30 1 108.0630 1106.26 108.0630 1106.26
28 29 31 1 103.0520 1157.45 103.0520 1157.45
28 29 33 1 103.0520 1157.45 103.0520 1157.45
30 29 31 1 108.0630 1106.26 108.0630 1106.26
30 29 33 1 108.0630 1106.26 108.0630 1106.26
31 29 33 1 103.0520 1157.45 103.0520 1157.45
29 31 32 1 115.3640 488.99 115.3640 488.99
29 33 34 1 115.3640 488.99 115.3640 488.99
3 35 36 1 106.5030 477.55 106.5030 477.55

[ dihedrals ]
; ai aj ak al fu phi0 kphi mult phi0 kphi mult
1 2 4 5 9 0.00 -1.4267 1 0.00 -1.4267 1
1 2 4 5 9 180.00 1.5816 2 180.00 1.5816 2
1 2 4 5 9 0.00 1.5816 3 0.00 1.5816 3
1 2 4 7 9 0.00 0.4812 1 0.00 0.4812 1
1 2 4 7 9 180.00 -1.4853 2 180.00 -1.4853 2
1 2 4 7 9 0.00 1.5104 3 0.00 1.5104 3
1 2 4 39 9 0.00 1.1924 1 0.00 1.1924 1
1 2 4 39 9 180.00 0.6694 2 180.00 0.6694 2
1 2 4 39 9 0.00 1.1924 3 0.00 1.1924 3
1 3 6 5 9 0.00 0.2134 1 0.00 0.2134 1
1 3 6 5 9 180.00 1.4267 2 180.00 1.4267 2
1 3 6 5 9 0.00 0.6945 3 0.00 0.6945 3
1 3 6 28 9 0.00 -1.4393 1 0.00 -1.4393 1
1 3 6 28 9 180.00 3.6777 2 180.00 3.6777 2
1 3 6 28 9 0.00 0.9958 3 0.00 0.9958 3
1 3 6 41 9 0.00 1.3389 1 0.00 1.3389 1
1 3 6 41 9 180.00 -1.3180 2 180.00 -1.3180 2
1 3 6 41 9 0.00 0.5523 3 0.00 0.5523 3
1 3 35 36 9 180.00 0.5648 2 180.00 0.5648 2
1 3 35 36 9 0.00 0.4937 3 0.00 0.4937 3
1 25 26 27 9 180.00 0.5648 2 180.00 0.5648 2
1 25 26 27 9 0.00 0.4937 3 0.00 0.4937 3
2 1 3 6 9 0.00 -1.4393 1 0.00 -1.4393 1
2 1 3 6 9 180.00 3.6777 2 180.00 3.6777 2
2 1 3 6 9 0.00 0.9958 3 0.00 0.9958 3
2 1 3 35 9 0.00 0.8535 1 0.00 0.8535 1
2 1 3 35 9 180.00 2.9246 2 180.00 2.9246 2
2 1 3 35 9 0.00 2.0083 3 0.00 2.0083 3
2 1 3 38 9 0.00 -1.3682 1 0.00 -1.3682 1
2 1 3 38 9 180.00 2.2426 2 180.00 2.2426 2
2 1 3 38 9 0.00 0.5858 3 0.00 0.5858 3
2 1 25 26 9 0.00 0.8535 1 0.00 0.8535 1
2 1 25 26 9 180.00 2.9246 2 180.00 2.9246 2
2 1 25 26 9 0.00 2.0083 3 0.00 2.0083 3
2 1 25 52 9 0.00 -1.3682 1 0.00 -1.3682 1
2 1 25 52 9 180.00 2.2426 2 180.00 2.2426 2
2 1 25 52 9 0.00 0.5858 3 0.00 0.5858 3
2 1 25 53 9 0.00 -1.3682 1 0.00 -1.3682 1
2 1 25 53 9 180.00 2.2426 2 180.00 2.2426 2
2 1 25 53 9 0.00 0.5858 3 0.00 0.5858 3
2 4 5 6 9 0.00 -1.4393 1 0.00 -1.4393 1
2 4 5 6 9 180.00 3.6777 2 180.00 3.6777 2
2 4 5 6 9 0.00 0.9958 3 0.00 0.9958 3
2 4 5 23 9 0.00 0.8535 1 0.00 0.8535 1
2 4 5 23 9 180.00 2.9246 2 180.00 2.9246 2
2 4 5 23 9 0.00 2.0083 3 0.00 2.0083 3
2 4 5 40 9 0.00 -1.3682 1 0.00 -1.3682 1
2 4 5 40 9 180.00 2.2426 2 180.00 2.2426 2
2 4 5 40 9 0.00 0.5858 3 0.00 0.5858 3
2 4 7 8 9 0.00 0.4812 1 0.00 0.4812 1
2 4 7 8 9 180.00 -1.4853 2 180.00 -1.4853 2
2 4 7 8 9 0.00 1.5104 3 0.00 1.5104 3
3 1 2 4 9 0.00 -1.4267 1 0.00 -1.4267 1
3 1 2 4 9 180.00 1.5816 2 180.00 1.5816 2
3 1 2 4 9 0.00 1.5816 3 0.00 1.5816 3
3 1 25 26 9 0.00 -1.4393 1 0.00 -1.4393 1
3 1 25 26 9 180.00 3.6777 2 180.00 3.6777 2
3 1 25 26 9 0.00 0.9958 3 0.00 0.9958 3
3 1 25 52 9 0.00 1.3389 1 0.00 1.3389 1
3 1 25 52 9 180.00 -1.3180 2 180.00 -1.3180 2
3 1 25 52 9 0.00 0.5523 3 0.00 0.5523 3
3 1 25 53 9 0.00 1.3389 1 0.00 1.3389 1
3 1 25 53 9 180.00 -1.3180 2 180.00 -1.3180 2
3 1 25 53 9 0.00 0.5523 3 0.00 0.5523 3
3 6 5 4 9 0.00 0.2134 1 0.00 0.2134 1
3 6 5 4 9 180.00 1.4267 2 180.00 1.4267 2
3 6 5 4 9 0.00 0.6945 3 0.00 0.6945 3
3 6 5 23 9 0.00 -1.4393 1 0.00 -1.4393 1
3 6 5 23 9 180.00 3.6777 2 180.00 3.6777 2
3 6 5 23 9 0.00 0.9958 3 0.00 0.9958 3
3 6 5 40 9 0.00 1.3389 1 0.00 1.3389 1
3 6 5 40 9 180.00 -1.3180 2 180.00 -1.3180 2
3 6 5 40 9 0.00 0.5523 3 0.00 0.5523 3
3 6 28 29 9 0.00 0.4184 3 0.00 0.4184 3
4 2 1 25 9 0.00 -1.4267 1 0.00 -1.4267 1
4 2 1 25 9 180.00 1.5816 2 180.00 1.5816 2
4 2 1 25 9 0.00 1.5816 3 0.00 1.5816 3
4 2 1 37 9 0.00 1.1924 1 0.00 1.1924 1
4 2 1 37 9 180.00 0.6694 2 180.00 0.6694 2
4 2 1 37 9 0.00 1.1924 3 0.00 1.1924 3
4 5 6 28 9 0.00 -1.4393 1 0.00 -1.4393 1
4 5 6 28 9 180.00 3.6777 2 180.00 3.6777 2
4 5 6 28 9 0.00 0.9958 3 0.00 0.9958 3
4 5 6 41 9 0.00 1.3389 1 0.00 1.3389 1
4 5 6 41 9 180.00 -1.3180 2 180.00 -1.3180 2
4 5 6 41 9 0.00 0.5523 3 0.00 0.5523 3
4 5 23 24 9 180.00 0.5648 2 180.00 0.5648 2
4 5 23 24 9 0.00 0.4937 3 0.00 0.4937 3
4 7 8 9 9 0.00 -1.4267 1 0.00 -1.4267 1
4 7 8 9 9 180.00 1.5816 2 180.00 1.5816 2
4 7 8 9 9 0.00 1.5816 3 0.00 1.5816 3
4 7 8 42 9 0.00 1.1924 1 0.00 1.1924 1
4 7 8 42 9 180.00 0.6694 2 180.00 0.6694 2
4 7 8 42 9 0.00 1.1924 3 0.00 1.1924 3
4 7 8 43 9 0.00 1.1924 1 0.00 1.1924 1
4 7 8 43 9 180.00 0.6694 2 180.00 0.6694 2
4 7 8 43 9 0.00 1.1924 3 0.00 1.1924 3
5 4 7 8 9 0.00 -1.4267 1 0.00 -1.4267 1
5 4 7 8 9 180.00 1.5816 2 180.00 1.5816 2
5 4 7 8 9 0.00 1.5816 3 0.00 1.5816 3
5 6 3 35 9 0.00 -1.4393 1 0.00 -1.4393 1
5 6 3 35 9 180.00 3.6777 2 180.00 3.6777 2
5 6 3 35 9 0.00 0.9958 3 0.00 0.9958 3
5 6 3 38 9 0.00 1.3389 1 0.00 1.3389 1
5 6 3 38 9 180.00 -1.3180 2 180.00 -1.3180 2
5 6 3 38 9 0.00 0.5523 3 0.00 0.5523 3
5 6 28 29 9 0.00 0.4184 3 0.00 0.4184 3
6 3 1 25 9 0.00 0.2134 1 0.00 0.2134 1
6 3 1 25 9 180.00 1.4267 2 180.00 1.4267 2
6 3 1 25 9 0.00 0.6945 3 0.00 0.6945 3
6 3 1 37 9 0.00 1.3389 1 0.00 1.3389 1
6 3 1 37 9 180.00 -1.3180 2 180.00 -1.3180 2
6 3 1 37 9 0.00 0.5523 3 0.00 0.5523 3
6 3 35 36 9 180.00 0.5648 2 180.00 0.5648 2
6 3 35 36 9 0.00 0.4937 3 0.00 0.4937 3
6 5 4 7 9 0.00 -1.4393 1 0.00 -1.4393 1
6 5 4 7 9 180.00 3.6777 2 180.00 3.6777 2
6 5 4 7 9 0.00 0.9958 3 0.00 0.9958 3
6 5 4 39 9 0.00 1.3389 1 0.00 1.3389 1
6 5 4 39 9 180.00 -1.3180 2 180.00 -1.3180 2
6 5 4 39 9 0.00 0.5523 3 0.00 0.5523 3
6 5 23 24 9 180.00 0.5648 2 180.00 0.5648 2
6 5 23 24 9 0.00 0.4937 3 0.00 0.4937 3
6 28 29 30 9 0.00 0.2092 3 0.00 0.2092 3
6 28 29 31 9 0.00 0.2092 3 0.00 0.2092 3
6 28 29 33 9 0.00 0.2092 3 0.00 0.2092 3
7 4 5 23 9 0.00 0.8535 1 0.00 0.8535 1
7 4 5 23 9 180.00 2.9246 2 180.00 2.9246 2
7 4 5 23 9 0.00 2.0083 3 0.00 2.0083 3
7 4 5 40 9 0.00 -1.3682 1 0.00 -1.3682 1
7 4 5 40 9 180.00 2.2426 2 180.00 2.2426 2
7 4 5 40 9 0.00 0.5858 3 0.00 0.5858 3
7 8 9 10 9 0.00 -1.4393 1 0.00 -1.4393 1
7 8 9 10 9 180.00 3.6777 2 180.00 3.6777 2
7 8 9 10 9 0.00 0.9958 3 0.00 0.9958 3
7 8 9 16 9 0.00 0.6276 3 0.00 0.6276 3
7 8 9 44 9 0.00 -1.3682 1 0.00 -1.3682 1
7 8 9 44 9 180.00 2.2426 2 180.00 2.2426 2
7 8 9 44 9 0.00 0.5858 3 0.00 0.5858 3
8 7 4 39 9 0.00 1.1924 1 0.00 1.1924 1
8 7 4 39 9 180.00 0.6694 2 180.00 0.6694 2
8 7 4 39 9 0.00 1.1924 3 0.00 1.1924 3
8 9 10 11 9 0.00 -0.6150 1 0.00 -0.6150 1
8 9 10 11 9 180.00 0.9163 2 180.00 0.9163 2
8 9 10 11 9 0.00 1.2217 3 0.00 1.2217 3
8 9 10 14 9 0.00 -1.4393 1 0.00 -1.4393 1
8 9 10 14 9 180.00 3.6777 2 180.00 3.6777 2
8 9 10 14 9 0.00 0.9958 3 0.00 0.9958 3
8 9 10 45 9 0.00 1.3389 1 0.00 1.3389 1
8 9 10 45 9 180.00 -1.3180 2 180.00 -1.3180 2
8 9 10 45 9 0.00 0.5523 3 0.00 0.5523 3
8 9 16 17 9 0.00 -2.1464 1 0.00 -2.1464 1
8 9 16 17 9 180.00 1.4518 2 180.00 1.4518 2
8 9 16 17 9 0.00 1.9832 3 0.00 1.9832 3
8 9 16 19 9 0.00 1.1548 1 0.00 1.1548 1
8 9 16 19 9 180.00 -0.7950 2 180.00 -0.7950 2
8 9 16 19 9 0.00 0.6820 3 0.00 0.6820 3
9 10 11 12 9 0.00 -1.0334 1 0.00 -1.0334 1
9 10 11 12 9 180.00 0.5732 2 180.00 0.5732 2
9 10 11 12 9 0.00 -1.3180 3 0.00 -1.3180 3
9 10 11 46 9 0.00 0.1548 1 0.00 0.1548 1
9 10 11 46 9 0.00 0.7489 3 0.00 0.7489 3
9 10 14 15 9 180.00 0.5648 2 180.00 0.5648 2
9 10 14 15 9 0.00 0.4937 3 0.00 0.4937 3
9 16 17 18 9 0.00 -0.6694 1 0.00 -0.6694 1
9 16 17 18 9 180.00 13.1670 2 180.00 13.1670 2
9 16 17 18 9 0.00 -0.3054 3 0.00 -0.3054 3
9 16 17 20 9 0.00 1.3556 1 0.00 1.3556 1
9 16 17 20 9 180.00 12.8825 2 180.00 12.8825 2
9 16 17 20 9 0.00 1.0627 3 0.00 1.0627 3
10 9 8 42 9 0.00 1.3389 1 0.00 1.3389 1
10 9 8 42 9 180.00 -1.3180 2 180.00 -1.3180 2
10 9 8 42 9 0.00 0.5523 3 0.00 0.5523 3
10 9 8 43 9 0.00 1.3389 1 0.00 1.3389 1
10 9 8 43 9 180.00 -1.3180 2 180.00 -1.3180 2
10 9 8 43 9 0.00 0.5523 3 0.00 0.5523 3
10 9 16 17 9 0.00 -2.1464 1 0.00 -2.1464 1
10 9 16 17 9 180.00 1.4518 2 180.00 1.4518 2
10 9 16 17 9 0.00 1.9832 3 0.00 1.9832 3
10 9 16 19 9 0.00 1.1548 1 0.00 1.1548 1
10 9 16 19 9 180.00 -0.7950 2 180.00 -0.7950 2
10 9 16 19 9 0.00 0.6820 3 0.00 0.6820 3
10 11 12 13 9 0.00 -0.8452 1 0.00 -0.8452 1
10 11 12 13 9 180.00 25.1040 2 180.00 25.1040 2
10 11 12 47 9 180.00 25.1040 2 180.00 25.1040 2
11 10 9 16 9 0.00 0.6276 3 0.00 0.6276 3
11 10 9 44 9 0.00 0.6736 1 0.00 0.6736 1
11 10 9 44 9 180.00 -0.8577 2 180.00 -0.8577 2
11 10 9 44 9 0.00 0.3012 3 0.00 0.3012 3
11 10 14 15 9 0.00 0.2134 1 0.00 0.2134 1
11 10 14 15 9 180.00 0.9623 2 180.00 0.9623 2
11 10 14 15 9 0.00 -0.2678 3 0.00 -0.2678 3
11 12 13 54 9 0.00 1.0502 1 0.00 1.0502 1
11 12 13 54 9 180.00 -0.8577 2 180.00 -0.8577 2
11 12 13 54 9 0.00 -1.1213 3 0.00 -1.1213 3
11 12 13 55 9 0.00 1.0502 1 0.00 1.0502 1
11 12 13 55 9 180.00 -0.8577 2 180.00 -0.8577 2
11 12 13 55 9 0.00 -1.1213 3 0.00 -1.1213 3
11 12 13 56 9 0.00 1.0502 1 0.00 1.0502 1
11 12 13 56 9 180.00 -0.8577 2 180.00 -0.8577 2
11 12 13 56 9 0.00 -1.1213 3 0.00 -1.1213 3
12 11 10 14 9 0.00 0.8870 1 0.00 0.8870 1
12 11 10 14 9 180.00 0.3515 2 180.00 0.3515 2
12 11 10 14 9 0.00 -1.8326 3 0.00 -1.8326 3
12 11 10 45 9 0.00 1.0502 1 0.00 1.0502 1
12 11 10 45 9 180.00 -0.8577 2 180.00 -0.8577 2
12 11 10 45 9 0.00 -1.1213 3 0.00 -1.1213 3
13 12 11 46 9 180.00 25.1040 2 180.00 25.1040 2
14 10 9 16 9 0.00 0.6276 3 0.00 0.6276 3
14 10 9 44 9 0.00 -1.3682 1 0.00 -1.3682 1
14 10 9 44 9 180.00 2.2426 2 180.00 2.2426 2
14 10 9 44 9 0.00 0.5858 3 0.00 0.5858 3
14 10 11 46 9 180.00 0.2845 2 180.00 0.2845 2
14 10 11 46 9 0.00 0.8284 3 0.00 0.8284 3
15 14 10 45 9 0.00 1.2468 1 0.00 1.2468 1
15 14 10 45 9 180.00 -0.5774 2 180.00 -0.5774 2
15 14 10 45 9 0.00 0.7238 3 0.00 0.7238 3
16 9 8 42 9 0.00 0.8912 3 0.00 0.8912 3
16 9 8 43 9 0.00 0.8912 3 0.00 0.8912 3
16 9 10 45 9 0.00 0.8912 3 0.00 0.8912 3
16 17 20 21 9 0.00 -1.9414 1 0.00 -1.9414 1
16 17 20 21 9 180.00 2.3263 2 180.00 2.3263 2
16 17 20 21 9 0.00 2.9037 3 0.00 2.9037 3
16 17 20 48 9 0.00 -0.8619 1 0.00 -0.8619 1
16 17 20 48 9 180.00 1.4477 2 180.00 1.4477 2
16 17 20 48 9 0.00 0.1799 3 0.00 0.1799 3
16 17 20 49 9 0.00 -0.8619 1 0.00 -0.8619 1
16 17 20 49 9 180.00 1.4477 2 180.00 1.4477 2
16 17 20 49 9 0.00 0.1799 3 0.00 0.1799 3
17 16 9 44 9 0.00 -4.3932 1 0.00 -4.3932 1
17 16 9 44 9 180.00 2.8493 2 180.00 2.8493 2
17 16 9 44 9 0.00 0.0460 3 0.00 0.0460 3
17 20 21 22 9 0.00 0.1381 1 0.00 0.1381 1
17 20 21 22 9 180.00 -0.3264 2 180.00 -0.3264 2
17 20 21 22 9 0.00 0.2971 3 0.00 0.2971 3
17 20 21 50 9 0.00 -0.5356 1 0.00 -0.5356 1
17 20 21 50 9 180.00 0.1213 2 180.00 0.1213 2
17 20 21 51 9 0.00 -0.5356 1 0.00 -0.5356 1
17 20 21 51 9 180.00 0.1213 2 180.00 0.1213 2
18 17 16 19 9 0.00 3.0041 1 0.00 3.0041 1
18 17 16 19 9 180.00 10.4056 2 180.00 10.4056 2
18 17 16 19 9 0.00 -0.9498 3 0.00 -0.9498 3
18 17 20 21 9 0.00 1.7238 1 0.00 1.7238 1
18 17 20 21 9 180.00 0.2929 2 180.00 0.2929 2
18 17 20 21 9 0.00 0.6820 3 0.00 0.6820 3
18 17 20 48 9 0.00 1.3807 1 0.00 1.3807 1
18 17 20 48 9 180.00 -2.9455 2 180.00 -2.9455 2
18 17 20 48 9 0.00 0.6443 3 0.00 0.6443 3
18 17 20 49 9 0.00 1.3807 1 0.00 1.3807 1
18 17 20 49 9 180.00 -2.9455 2 180.00 -2.9455 2
18 17 20 49 9 0.00 0.6443 3 0.00 0.6443 3
19 16 9 44 9 0.00 -1.2887 1 0.00 -1.2887 1
19 16 9 44 9 0.00 0.5732 3 0.00 0.5732 3
19 16 17 20 9 0.00 -0.6150 1 0.00 -0.6150 1
19 16 17 20 9 180.00 12.1420 2 180.00 12.1420 2
19 16 17 20 9 0.00 2.8075 3 0.00 2.8075 3
20 21 22 57 9 0.00 1.3389 1 0.00 1.3389 1
20 21 22 57 9 180.00 -1.3180 2 180.00 -1.3180 2
20 21 22 57 9 0.00 0.5523 3 0.00 0.5523 3
20 21 22 58 9 0.00 1.3389 1 0.00 1.3389 1
20 21 22 58 9 180.00 -1.3180 2 180.00 -1.3180 2
20 21 22 58 9 0.00 0.5523 3 0.00 0.5523 3
20 21 22 59 9 0.00 1.3389 1 0.00 1.3389 1
20 21 22 59 9 180.00 -1.3180 2 180.00 -1.3180 2
20 21 22 59 9 0.00 0.5523 3 0.00 0.5523 3
22 21 20 48 9 0.00 1.3389 1 0.00 1.3389 1
22 21 20 48 9 180.00 -1.3180 2 180.00 -1.3180 2
22 21 20 48 9 0.00 0.5523 3 0.00 0.5523 3
22 21 20 49 9 0.00 1.3389 1 0.00 1.3389 1
22 21 20 49 9 180.00 -1.3180 2 180.00 -1.3180 2
22 21 20 49 9 0.00 0.5523 3 0.00 0.5523 3
23 5 4 39 9 0.00 -1.3682 1 0.00 -1.3682 1
23 5 4 39 9 180.00 2.2426 2 180.00 2.2426 2
23 5 4 39 9 0.00 0.5858 3 0.00 0.5858 3
23 5 6 28 9 0.00 0.8535 1 0.00 0.8535 1
23 5 6 28 9 180.00 2.9246 2 180.00 2.9246 2
23 5 6 28 9 0.00 2.0083 3 0.00 2.0083 3
23 5 6 41 9 0.00 -1.3682 1 0.00 -1.3682 1
23 5 6 41 9 180.00 2.2426 2 180.00 2.2426 2
23 5 6 41 9 0.00 0.5858 3 0.00 0.5858 3
24 23 5 40 9 0.00 1.2468 1 0.00 1.2468 1
24 23 5 40 9 180.00 -0.5774 2 180.00 -0.5774 2
24 23 5 40 9 0.00 0.7238 3 0.00 0.7238 3
25 1 3 35 9 0.00 -1.4393 1 0.00 -1.4393 1
25 1 3 35 9 180.00 3.6777 2 180.00 3.6777 2
25 1 3 35 9 0.00 0.9958 3 0.00 0.9958 3
25 1 3 38 9 0.00 1.3389 1 0.00 1.3389 1
25 1 3 38 9 180.00 -1.3180 2 180.00 -1.3180 2
25 1 3 38 9 0.00 0.5523 3 0.00 0.5523 3
26 25 1 37 9 0.00 -1.3682 1 0.00 -1.3682 1
26 25 1 37 9 180.00 2.2426 2 180.00 2.2426 2
26 25 1 37 9 0.00 0.5858 3 0.00 0.5858 3
27 26 25 52 9 0.00 1.2468 1 0.00 1.2468 1
27 26 25 52 9 180.00 -0.5774 2 180.00 -0.5774 2
27 26 25 52 9 0.00 0.7238 3 0.00 0.7238 3
27 26 25 53 9 0.00 1.2468 1 0.00 1.2468 1
27 26 25 53 9 180.00 -0.5774 2 180.00 -0.5774 2
27 26 25 53 9 0.00 0.7238 3 0.00 0.7238 3
28 6 3 35 9 0.00 0.8535 1 0.00 0.8535 1
28 6 3 35 9 180.00 2.9246 2 180.00 2.9246 2
28 6 3 35 9 0.00 2.0083 3 0.00 2.0083 3
28 6 3 38 9 0.00 -1.3682 1 0.00 -1.3682 1
28 6 3 38 9 180.00 2.2426 2 180.00 2.2426 2
28 6 3 38 9 0.00 0.5858 3 0.00 0.5858 3
28 6 5 40 9 0.00 -1.3682 1 0.00 -1.3682 1
28 6 5 40 9 180.00 2.2426 2 180.00 2.2426 2
28 6 5 40 9 0.00 0.5858 3 0.00 0.5858 3
28 29 31 32 9 0.00 -3.3932 1 0.00 -3.3932 1
28 29 31 32 9 180.00 0.4268 2 180.00 0.4268 2
28 29 31 32 9 0.00 0.9163 3 0.00 0.9163 3
28 29 33 34 9 0.00 -3.3932 1 0.00 -3.3932 1
28 29 33 34 9 180.00 0.4268 2 180.00 0.4268 2
28 29 33 34 9 0.00 0.9163 3 0.00 0.9163 3
29 28 6 41 9 0.00 0.4184 3 0.00 0.4184 3
30 29 31 32 9 0.00 3.3807 1 0.00 3.3807 1
30 29 31 32 9 180.00 0.8870 2 180.00 0.8870 2
30 29 31 32 9 0.00 0.4017 3 0.00 0.4017 3
30 29 33 34 9 0.00 3.3807 1 0.00 3.3807 1
30 29 33 34 9 180.00 0.8870 2 180.00 0.8870 2
30 29 33 34 9 0.00 0.4017 3 0.00 0.4017 3
31 29 33 34 9 0.00 -3.3932 1 0.00 -3.3932 1
31 29 33 34 9 180.00 0.4268 2 180.00 0.4268 2
31 29 33 34 9 0.00 0.9163 3 0.00 0.9163 3
32 31 29 33 9 0.00 -3.3932 1 0.00 -3.3932 1
32 31 29 33 9 180.00 0.4268 2 180.00 0.4268 2
32 31 29 33 9 0.00 0.9163 3 0.00 0.9163 3
35 3 1 37 9 0.00 -1.3682 1 0.00 -1.3682 1
35 3 1 37 9 180.00 2.2426 2 180.00 2.2426 2
35 3 1 37 9 0.00 0.5858 3 0.00 0.5858 3
35 3 6 41 9 0.00 -1.3682 1 0.00 -1.3682 1
35 3 6 41 9 180.00 2.2426 2 180.00 2.2426 2
35 3 6 41 9 0.00 0.5858 3 0.00 0.5858 3
36 35 3 38 9 0.00 1.2468 1 0.00 1.2468 1
36 35 3 38 9 180.00 -0.5774 2 180.00 -0.5774 2
36 35 3 38 9 0.00 0.7238 3 0.00 0.7238 3
37 1 3 38 9 0.00 0.5941 1 0.00 0.5941 1
37 1 3 38 9 180.00 -2.8995 2 180.00 -2.8995 2
37 1 3 38 9 0.00 0.6569 3 0.00 0.6569 3
37 1 25 52 9 0.00 0.5941 1 0.00 0.5941 1
37 1 25 52 9 180.00 -2.8995 2 180.00 -2.8995 2
37 1 25 52 9 0.00 0.6569 3 0.00 0.6569 3
37 1 25 53 9 0.00 0.5941 1 0.00 0.5941 1
37 1 25 53 9 180.00 -2.8995 2 180.00 -2.8995 2
37 1 25 53 9 0.00 0.6569 3 0.00 0.6569 3
38 3 6 41 9 0.00 0.5941 1 0.00 0.5941 1
38 3 6 41 9 180.00 -2.8995 2 180.00 -2.8995 2
38 3 6 41 9 0.00 0.6569 3 0.00 0.6569 3
39 4 5 40 9 0.00 0.5941 1 0.00 0.5941 1
39 4 5 40 9 180.00 -2.8995 2 180.00 -2.8995 2
39 4 5 40 9 0.00 0.6569 3 0.00 0.6569 3
40 5 6 41 9 0.00 0.5941 1 0.00 0.5941 1
40 5 6 41 9 180.00 -2.8995 2 180.00 -2.8995 2
40 5 6 41 9 0.00 0.6569 3 0.00 0.6569 3
42 8 9 44 9 0.00 0.5941 1 0.00 0.5941 1
42 8 9 44 9 180.00 -2.8995 2 180.00 -2.8995 2
42 8 9 44 9 0.00 0.6569 3 0.00 0.6569 3
43 8 9 44 9 0.00 0.5941 1 0.00 0.5941 1
43 8 9 44 9 180.00 -2.8995 2 180.00 -2.8995 2
43 8 9 44 9 0.00 0.6569 3 0.00 0.6569 3
44 9 10 45 9 0.00 0.5941 1 0.00 0.5941 1
44 9 10 45 9 180.00 -2.8995 2 180.00 -2.8995 2
44 9 10 45 9 0.00 0.6569 3 0.00 0.6569 3
45 10 11 46 9 0.00 -1.0962 1 0.00 -1.0962 1
45 10 11 46 9 180.00 -0.4770 2 180.00 -0.4770 2
45 10 11 46 9 0.00 0.4351 3 0.00 0.4351 3
46 11 12 47 9 180.00 25.1040 2 180.00 25.1040 2
47 12 13 54 9 0.00 -1.0962 1 0.00 -1.0962 1
47 12 13 54 9 180.00 -0.4770 2 180.00 -0.4770 2
47 12 13 54 9 0.00 0.4351 3 0.00 0.4351 3
47 12 13 55 9 0.00 -1.0962 1 0.00 -1.0962 1
47 12 13 55 9 180.00 -0.4770 2 180.00 -0.4770 2
47 12 13 55 9 0.00 0.4351 3 0.00 0.4351 3
47 12 13 56 9 0.00 -1.0962 1 0.00 -1.0962 1
47 12 13 56 9 180.00 -0.4770 2 180.00 -0.4770 2
47 12 13 56 9 0.00 0.4351 3 0.00 0.4351 3
48 20 21 50 9 0.00 0.5941 1 0.00 0.5941 1
48 20 21 50 9 180.00 -2.8995 2 180.00 -2.8995 2
48 20 21 50 9 0.00 0.6569 3 0.00 0.6569 3
48 20 21 51 9 0.00 0.5941 1 0.00 0.5941 1
48 20 21 51 9 180.00 -2.8995 2 180.00 -2.8995 2
48 20 21 51 9 0.00 0.6569 3 0.00 0.6569 3
49 20 21 50 9 0.00 0.5941 1 0.00 0.5941 1
49 20 21 50 9 180.00 -2.8995 2 180.00 -2.8995 2
49 20 21 50 9 0.00 0.6569 3 0.00 0.6569 3
49 20 21 51 9 0.00 0.5941 1 0.00 0.5941 1
49 20 21 51 9 180.00 -2.8995 2 180.00 -2.8995 2
49 20 21 51 9 0.00 0.6569 3 0.00 0.6569 3
50 21 22 57 9 0.00 0.5941 1 0.00 0.5941 1
50 21 22 57 9 180.00 -2.8995 2 180.00 -2.8995 2
50 21 22 57 9 0.00 0.6569 3 0.00 0.6569 3
50 21 22 58 9 0.00 0.5941 1 0.00 0.5941 1
50 21 22 58 9 180.00 -2.8995 2 180.00 -2.8995 2
50 21 22 58 9 0.00 0.6569 3 0.00 0.6569 3
50 21 22 59 9 0.00 0.5941 1 0.00 0.5941 1
50 21 22 59 9 180.00 -2.8995 2 180.00 -2.8995 2
50 21 22 59 9 0.00 0.6569 3 0.00 0.6569 3
51 21 22 57 9 0.00 0.5941 1 0.00 0.5941 1
51 21 22 57 9 180.00 -2.8995 2 180.00 -2.8995 2
51 21 22 57 9 0.00 0.6569 3 0.00 0.6569 3
51 21 22 58 9 0.00 0.5941 1 0.00 0.5941 1
51 21 22 58 9 180.00 -2.8995 2 180.00 -2.8995 2
51 21 22 58 9 0.00 0.6569 3 0.00 0.6569 3
51 21 22 59 9 0.00 0.5941 1 0.00 0.5941 1
51 21 22 59 9 180.00 -2.8995 2 180.00 -2.8995 2
51 21 22 59 9 0.00 0.6569 3 0.00 0.6569 3

[ dihedrals ]
; ai aj ak al fu xi0 kxi xi0 kxi
1 3 2 25 2 0.00 0.0000 0.00 0.0000
1 3 2 37 2 0.00 0.0000 0.00 0.0000
4 7 2 5 2 0.00 0.0000 0.00 0.0000
4 5 2 39 2 0.00 0.0000 0.00 0.0000
3 6 1 35 2 0.00 0.0000 0.00 0.0000
3 35 1 38 2 0.00 0.0000 0.00 0.0000
8 9 7 42 2 0.00 0.0000 0.00 0.0000
8 9 7 43 2 0.00 0.0000 0.00 0.0000
9 16 8 10 2 0.00 0.0000 0.00 0.0000
9 10 8 44 2 0.00 0.0000 0.00 0.0000
10 11 9 14 2 0.00 0.0000 0.00 0.0000
10 14 9 45 2 0.00 0.0000 0.00 0.0000
11 12 10 46 2 0.00 7.8324 0.00 7.8324
12 13 11 47 2 0.00 7.8324 0.00 7.8324
16 17 9 19 2 0.00 -12.0416 0.00 -12.0416
17 20 16 18 2 0.00 77.6885 0.00 77.6885
20 21 17 48 2 0.00 0.0000 0.00 0.0000
20 21 17 49 2 0.00 0.0000 0.00 0.0000
21 22 20 50 2 0.00 0.0000 0.00 0.0000
21 22 20 51 2 0.00 0.0000 0.00 0.0000
5 6 4 23 2 0.00 0.0000 0.00 0.0000
5 23 4 40 2 0.00 0.0000 0.00 0.0000
25 26 1 52 2 0.00 0.0000 0.00 0.0000
25 26 1 53 2 0.00 0.0000 0.00 0.0000
6 5 3 28 2 0.00 0.0000 0.00 0.0000
6 5 3 41 2 0.00 0.0000 0.00 0.0000
29 33 28 31 2 0.00 0.0000 0.00 0.0000
29 33 28 30 2 0.00 0.0000 0.00 0.0000
13 54 12 55 2 0.00 0.0000 0.00 0.0000
13 54 12 56 2 0.00 0.0000 0.00 0.0000
22 57 21 58 2 0.00 0.0000 0.00 0.0000
22 57 21 59 2 0.00 0.0000 0.00 0.0000

#ifdef POSRES_LIGAND
[ position_restraints ]
; atom type fx fy fz
1 1 1000 1000 1000
2 1 1000 1000 1000
3 1 1000 1000 1000
4 1 1000 1000 1000
5 1 1000 1000 1000
6 1 1000 1000 1000
7 1 1000 1000 1000
8 1 1000 1000 1000
9 1 1000 1000 1000
10 1 1000 1000 1000
11 1 1000 1000 1000
12 1 1000 1000 1000
13 1 1000 1000 1000
14 1 1000 1000 1000
16 1 1000 1000 1000
17 1 1000 1000 1000
18 1 1000 1000 1000
20 1 1000 1000 1000
21 1 1000 1000 1000
22 1 1000 1000 1000
23 1 1000 1000 1000
25 1 1000 1000 1000
26 1 1000 1000 1000
28 1 1000 1000 1000
29 1 1000 1000 1000
30 1 1000 1000 1000
31 1 1000 1000 1000
33 1 1000 1000 1000
35 1 1000 1000 1000
#endif

4

Hi,

You need to provide also the topol.top (the file where SGC_fix.itp is included). Topology files has its own hierarchy (which must be followed) consists of three levels: force field, molecules and system level.
The directives [ atomtypes ] [ pairtypes ] belong to force field level and those has to be before any directives of molecule level (e.i [moleculetype ]).

Alessandra

5

Dear Dr.Avilla

Sorry for my mistake

I meant from topology file was .itp file. You replied me before to see SGC_fix.itp file carefully to check atomtypes C=C and SO2 are not defined more than one time in the [atomtype] directive and avoid to define the atomtype more than once. I checked it and did not find any strange thing in that. Another thing that I needed to be checked if it is done correctly was, modifying’ the topolog file generated by pdb2gmx. I added the statement ’ #include “SGC-fix.itp” ’ at the top of the topol.top file between parent force field and [moleculetype] directive and added the line of ’ SGC-fix 1 ’ in the [molecules] section at the bottom of the topol.top file, right after lines indicating the number of protein molecules.

However I checked SGC_fix.itp file I can not find the problem.

These are the .pdb and .mol2 and .itp files of small organic molecule that https://www.swissparam.ch/ provided. I used https://www.swissparam.ch/SwissParam_gromacs_tutorial.html to do all the required modifyings step by step.

I would be grateful if you can help me to find where the problem is exactly.

Sincerely

Farial

(Attachment SGC_fix.itp is missing)

(Attachment SGC_fix.mol2 is missing)

(Attachment SGC_fix.pdb is missing)

6

Sorry for late answer. But attachment are missing. Better to use a link to the file (for example using googledocs). Do you have also a topol.top file? Please provide it.
Thanks
Alessandra

7

Dear Dr.Alesandra

Thank you for replying
I provided all the files related to my ligand at https://docs.google.com/document/d/1zmt_bbCYeYMcLg7dnYFTqrhRvl2kIaBKp8rKVvc0ja0/edit
and this is the topology file :

;
; File ‘topol.top’ was generated
; By user: vaio (1000)
; On host: vaio-VPCEA42EG
; At date: Sat Oct 16 21:39:04 2021

;
; This is a standalone topology file
;
; Created by:
; :-) GROMACS - gmx pdb2gmx, 2016.4 (-:
;
; Executable: /usr/local/gromacs/bin/gmx
; Data prefix: /usr/local/gromacs
; Working dir: /media/vaio/Apacer PHD/ARSA/docking results/SGC/WT
; Command line:
; gmx pdb2gmx -f ARSA.pdb -o ARSA.gro -ignh
; Force field was read from current directory or a relative path - path added.
;

; Include forcefield parameters
#include “./charmm27.ff/forcefield.itp”

; Include chain topologies
#include “WTSGC.itp”
#include “topol_pro_chain_A.itp”

; Include water topology
#include “./charmm27.ff/tip3p.itp”

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include “./charmm27.ff/ions.itp”

[ system ]
; Name
Protein in water

[ molecules ]
; Compound #mols
Protein_chain_A 1
WTSGC 1
SOL 18250

Thanks in advance
Farial

8

Hi
I am not allowed to see the files, can you change your share permission
Thank you
Alessandra

9

Oh sorry

I changed it to anyone. Now you can see it

Sincerely
Farial

10

Hi,
sorry I am a little confuse. You reported a warning concerning the file SGC_fix.itp , but this file is not in your topol.top file (reported in your post).
In which file is SGC_fix.itp included ?
I saw that C=C and SO2 are already defined in WTSGC.itp, thus if you have included somewhere also SGC_fix.itp ( and C=C and SO2 are defined there, as you wrote at the begin) then there is the duplication.
I hope it helps
Alessandra

11

Dear Allensadra

Sorry for that

I forgot to inform you I renamed the ligand itp file from WTSGC_fix.itp to WTSGC.itp
Thw warnings I sent before related to when the ligand itp file was named SGC_fix.itp . I just renamed it . That’s it.
I have not included the ligand itp file more than once in topol.top file either as WTSGC_fix.itp or as WTSGC.itp
But I dont know how come get this warning :

Thanks in advance
Farial

12

You are using a copy of the force field in the working directory rather than the standard ($GMXLIB) location. Is it modified in some way? What happens when you use the standard force field directory?

13

Dera Justin

Thank you for replying

I have a protein with unusual residue named FGL(formyl glycine). So I had to use ‘https://www.swisssidechain.ch/MD/gromacs.php’ .
all the steps I did are:
copied standard charmm27.ff from ‘/usr/local/gromacs/share/gromacs/top’ in the working directory ‘/media/vaio/Apacer PHD/ARSA/docking results/SGC/WT’ and then replaced some files by the ones in swisssidechain-gromacs including aminoacid.rtp, aminoacid.hdp, gb.itp, ffbounded.itp, ffnonbounded.itp and atomtype.atp. finally placed residuetypes.dat in ‘/media/vaio/Apacer PHD/ARSA/docking results/SGC/WT’. If your mean of modification are the same I did, yes I modified that.

MD production of my protein was done successfully . but now I have problem with my ligand in complex to the protein. I applied ‘https://www.swissparam.ch/’ to obtain topology and parameters for the small organic molecul named SGC .

all the steps I did are:
SGC.mol2 was generated using UCSF chimera with all hydrogens
then uploaded to this server to get SGC.itp and SGC.pdb
topol.top file generated by odb2gmx was done by adding SGC.itp at the top of that and adding SGC 1 at the bottom of that.

when I issued gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr

I got 2 warnings:

NOTE 1 [file ions.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.

Setting the LD random seed to 1794072544

WARNING 1 [file SGC.itp, line 11]:
Overriding atomtype C=C

WARNING 2 [file SGC.itp, line 17]:
Overriding atomtype SO2

Generated 28441 of the 28441 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 1
Generated 25311 of the 28441 1-4 parameter combinations

14

I suspect the issue is that by doing so, you incorporated new atom types into ffnonbonded.itp, hence the error about them being re-defined by another topology.

15

Dear Justin

Thank you for your reply

Yes I got it. So what should I do now ?

16

You do not need to re-introduce parameters in a molecule .itp file if they already exist in the parent force field. Delete the redundancies from the ligand topology.

17

Dera Justin

I deleted atomtypes c=c and so2 from [ atomtypes ] directive of WTSGC.itp file but when issued the

gmx grompp -f ions.mdp -c solv.gro -p topol.top -o ions.tpr
I got the error again

Program: gmx grompp, version 2016.4
Source file: src/gromacs/gmxpreprocess/topio.cpp (line 762)

Fatal error:
Syntax error - File WTSGC.itp, line 7
Last line read:
'[ atomtypes ] ’
Invalid order for directive atomtypes

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors

18

Did you visit the link suggested to you in the error message? The solution is there :)

19

Dear Justin

I solved the problem finally. Thank you so much for all of your guidance

with best regards
Farial

20

Dear Dr.Lemkul

I ran a simulation on my complex using Gromacs 2020.1 on the server in university and now I need to analyze it on my PC using gromacs 2016.4.

when issued the command

gmx trjconv -f .xtc -s .tpr -o nopbc.xtc -pbc mol -center -ur compact
got this error:
reading tpx file (md_0_1.tpr) version 119 with version 110 program
Is there anyway to solve this problem except updating the gromacs on my PC?

Thanks in advance
Farial