trying to create heme.params

[Anonymous]

Following advice on a thread from a year ago, I created a mol2 file from a heme ligand pdb. When I try to create the params file, it told me:
/usr/ros/rosetta_source/src/python/apps/public/molfile_to_params.py hemf.mol2
Traceback (most recent call last):
File "/usr/ros/rosetta_source/src/python/apps/public/molfile_to_params.py", line 1323, in ?
sys.exit(main(sys.argv[1:]))
File "/usr/ros/rosetta_source/src/python/apps/public/molfile_to_params.py", line 1254, in main
molfiles = list(read_tripos_mol2(infile, do_find_rings=False))
File "/usr/ros/rosetta_source/src/python/rosetta_py/io/mdl_molfile.py", line 409, in read_tripos_mol2
bond = Bond(atom1, atom2, order)
UnboundLocalError: local variable 'order' referenced before assignment
This is my .mol2 file, created with Schrodinger Maestro:

@MOLECULE
hemef
73 80 1
SMALL
USER_CHARGES

@ATOM
1 FE 19.1190 65.4070 56.8290 Fe 1 HEM 0.0000
2 CHA 17.0470 62.7190 57.1540 C.ar 1 HEM 0.0000
3 CHB 16.4190 67.4810 57.7270 C.ar 1 HEM 0.0000
4 CHC 21.0130 68.2620 56.4290 C.ar 1 HEM 0.0000
5 CHD 21.7380 63.4830 56.2500 C.ar 1 HEM 0.0000
6 NA 17.1350 65.1680 57.3130 N.pl3 1 HEM 0.0000
7 C1A 16.5050 63.9470 57.4330 C.ar 1 HEM 0.0000
8 C2A 15.1490 64.1640 57.9130 C.ar 1 HEM 0.0000
9 C3A 14.9710 65.4710 58.0580 C.ar 1 HEM 0.0000
10 C4A 16.2030 66.1290 57.6920 C.ar 1 HEM 0.0000
11 CMA 13.6750 66.1800 58.5550 C.3 1 HEM 0.0000
12 CAA 14.1020 63.0530 58.1860 C.3 1 HEM 0.0000
13 CBA 13.9960 62.7510 59.6890 C.3 1 HEM 0.0000
14 CGA 15.2090 61.9910 60.1930 C.2 1 HEM 0.0000
15 O1A 15.6490 61.0120 59.5330 O.co2 1 HEM 0.0000
16 O2A 15.7370 62.3640 61.2680 O.co2 1 HEM 0.0000
17 NB 18.7780 67.4530 57.0530 N.ar 1 HEM 0.0000
18 C1B 17.5960 68.0960 57.4100 C.ar 1 HEM 0.0000
19 C2B 17.8130 69.5200 57.3740 C.ar 1 HEM 0.0000
20 C3B 19.0770 69.7210 57.0060 C.ar 1 HEM 0.0000
21 C4B 19.7010 68.4440 56.7980 C.ar 1 HEM 0.0000
22 CMB 16.7570 70.5990 57.7080 C.3 1 HEM 0.0000
23 CAB 19.7940 71.0690 56.8290 C.2 1 HEM 0.0000
24 CBB 19.8070 71.6500 55.6320 C.2 1 HEM 0.0000
25 NC 21.0040 65.8140 56.4510 N.pl3 1 HEM 0.0000
26 C1C 21.6100 67.0410 56.2600 C.ar 1 HEM 0.0000
27 C2C 22.9730 66.8090 55.8440 C.ar 1 HEM 0.0000
28 C3C 23.1510 65.4820 55.7750 C.ar 1 HEM 0.0000
29 C4C 21.9190 64.8410 56.1570 C.ar 1 HEM 0.0000
30 CMC 24.0060 67.9050 55.4980 C.3 1 HEM 0.0000
31 CAC 24.4270 64.7210 55.3760 C.2 1 HEM 0.0000
32 CBC 25.3480 65.2740 54.5870 C.2 1 HEM 0.0000
33 ND 19.3440 63.4210 56.7510 N.ar 1 HEM 0.0000
34 C1D 20.5630 62.8270 56.4500 C.ar 1 HEM 0.0000
35 C2D 20.3820 61.4080 56.3640 C.ar 1 HEM 0.0000
36 C3D 18.9300 61.1670 56.6350 C.ar 1 HEM 0.0000
37 C4D 18.3510 62.4640 56.8600 C.ar 1 HEM 0.0000
38 CMD 21.4450 60.3320 56.0330 C.3 1 HEM 0.0000
39 CAD 18.2230 59.7960 56.6210 C.3 1 HEM 0.0000
40 CBD 17.6140 59.6320 55.2290 C.3 1 HEM 0.0000
41 CGD 16.9170 58.2940 55.1570 C.2 1 HEM 0.0000
42 O1D 17.3500 57.4400 54.3490 O.co2 1 HEM 0.0000
43 O2D 15.9500 58.0860 55.9160 O.co2 1 HEM 0.0000
44 HHA 16.4200 61.8390 57.1550 H 1 HEM 0.0000
45 HHB 15.6220 68.1480 58.0230 H 1 HEM 0.0000
46 HHC 21.6480 69.1180 56.2510 H 1 HEM 0.0000
47 HHD 22.5850 62.8180 56.1620 H 1 HEM 0.0000
48 HMA1 13.8330 67.2580 58.5680 H 1 HEM 0.0000
49 HMA2 12.8500 65.9420 57.8840 H 1 HEM 0.0000
50 HMA3 13.4350 65.8360 59.5610 H 1 HEM 0.0000
51 HAA1 13.1260 63.3770 57.8260 H 1 HEM 0.0000
52 HAA2 14.3960 62.1410 57.6670 H 1 HEM 0.0000
53 HBA1 13.9220 63.6860 60.2440 H 1 HEM 0.0000
54 HBA2 13.1090 62.1460 59.8770 H 1 HEM 0.0000
55 HMB1 17.2000 71.5890 57.5960 H 1 HEM 0.0000
56 HMB2 15.9100 70.5020 57.0290 H 1 HEM 0.0000
57 HMB3 16.4150 70.4680 58.7350 H 1 HEM 0.0000
58 HAB 20.2810 71.5360 57.6720 H 1 HEM 0.0000
59 HBB1 20.3080 72.5970 55.4970 H 1 HEM 0.0000
60 HBB2 19.3170 71.1740 54.7960 H 1 HEM 0.0000
61 HMC1 24.9510 67.4390 55.2170 H 1 HEM 0.0000
62 HMC2 23.6360 68.5050 54.6660 H 1 HEM 0.0000
63 HMC3 24.1610 68.5460 56.3660 H 1 HEM 0.0000
64 HAC 24.5920 63.7160 55.7370 H 1 HEM 0.0000
65 HBC1 26.2350 64.7190 54.3210 H 1 HEM 0.0000
66 HBC2 25.2070 66.2770 54.2130 H 1 HEM 0.0000
67 HMD1 20.9810 59.3460 56.0480 H 1 HEM 0.0000
68 HMD2 21.8600 60.5230 55.0430 H 1 HEM 0.0000
69 HMD3 22.2430 60.3690 56.7740 H 1 HEM 0.0000
70 HAD1 18.9500 59.0090 56.8210 H 1 HEM 0.0000
71 HAD2 17.4490 59.7780 57.3880 H 1 HEM 0.0000
72 HBD1 16.8960 60.4320 55.0490 H 1 HEM 0.0000
73 HBD2 18.4030 59.6780 54.4790 H 1 HEM 0.0000
@BOND
1 1 6 nc
2 1 17 nc
3 1 25 nc
4 1 33 nc
5 2 7 ar
6 2 37 ar
7 2 44 1
8 3 10 ar
9 3 18 ar
10 3 45 1
11 4 21 ar
12 4 26 ar
13 4 46 1
14 5 29 ar
15 5 34 ar
16 5 47 1
17 6 7 ar
18 6 10 ar
19 7 8 ar
20 8 9 ar
21 8 12 1
22 9 10 ar
23 9 11 1
24 11 48 1
25 11 49 1
26 11 50 1
27 12 13 1
28 12 51 1
29 12 52 1
30 13 14 1
31 13 53 1
32 13 54 1
33 14 15 2
34 14 16 1
35 17 18 ar
36 17 21 ar
37 18 19 ar
38 19 20 ar
39 19 22 1
40 20 21 ar
41 20 23 1
42 22 55 1
43 22 56 1
44 22 57 1
45 23 24 2
46 23 58 1
47 24 59 1
48 24 60 1
49 25 26 ar
50 25 29 ar
51 26 27 ar
52 27 28 ar
53 27 30 1
54 28 29 ar
55 28 31 1
56 30 61 1
57 30 62 1
58 30 63 1
59 31 32 2
60 31 64 1
61 32 65 1
62 32 66 1
63 33 34 ar
64 33 37 ar
65 34 35 ar
66 35 36 ar
67 35 38 1
68 36 37 ar
69 36 39 1
70 38 67 1
71 38 68 1
72 38 69 1
73 39 40 1
74 39 70 1
75 39 71 1
76 40 41 1
77 40 72 1
78 40 73 1
79 41 42 2
80 41 43 1
@SUBSTRUCTURE
1 HEM 1 GROUP 0 B **** 0 ROOT
Can someone see what’s wrong with it? I don’t have access to Tripos software to create the file. I’d welcome suggestions for an alternative conversion routine that is palatable to Rosetta.

Thanks!
Irene Newhouse

[Anonymous]

Hi Irene,

I ran molfile_to_params on the file you sent and was able to reproduce your error. I tried to visualize the molecule using MOE and was unable. I then opened the molecule up in pymol and was able to view it. I saved the molecule as a *.mol file and was able to use the mol_to_params script to generate a params file for it.

In general, molfile_to_params chokes on *.mol2 formats, even though it should support them. I suggest saving whatever molecules you make in the *.mol format.

Steven C

[Anonymous]

For what it’s worth, I’ve never had any issues with .mol2 files, at least on the OpenBabel/Avogadro produced structures I’ve used.

The particular issue you’re running into is the nc bond type to the iron is not currently recognized by molfile_to_params (although it is a valid bond type by the mol2 standard). I can update the code in the development version, but for your purposes I’ll suggest either using the .mol format as Steven suggests, or, if you want to use the user supplied charges in the .mol2 file, hand edit the .mol2 file to change the nc bond types to single bonds (“1”). I admit that might not be ideal, but it should result in a ligand topology file which works adequately.

Rocco Moretti

[Anonymous]

Thanks so much! I tried saving in .mol format, but molfile_to_params.py didn’t like the aromaticity specifications & refused to do the conversion. So I edited the mol2 file as suggested – replace nc with 1 – and that worked just fine (though with several warnings about how unproteinlike the system is).

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