Generating .params for a modified DNA residue

[JernejHirci]

Hello!

Does anyone have experience generating a .params file for a modified DNA residue? I have the following system I am trying to dock/score: a complex of protein with a dsDNA that has one residue modified (Adenine -> Ethenoadenine - EDA).

I have tried to generate .params file, but I always get some sort of an error/later error (my .mol2 file im running on is below). If i use "molfile_to_params_polymer.py" I get this error:

rosetta/source/scripts/python/public/molfile_to_params_polymer/IO_functions.py", line 519, in write_poly_param_file
nbb.input_stub1, nbb.input_stub2, nbb.input_stub3 = nbb, cabb, cbb
AttributeError: 'int' object has no attribute 'input_stub1'

I tried using just molfile_to_params.py and manually adjusting the .params file/using LLMs to help me, but it always leads to some downstream errors when docking/scoring. If anyone has solved/dealt with this I would really appreciate if you could help me out, thanks!

Mol2 file:

@MOLECULE
EDA_only_h_added.pdb
37 40 0 0 0
SMALL
GASTEIGER

@ATOM
1 P -20.9960 34.4410 9.3290 P.3 7 EDA7 0.3291
2 OP1 -21.9830 34.6480 10.4130 O.3 7 EDA7 -0.3278
3 OP2 -21.2290 35.0620 8.0020 O.3 7 EDA7 -0.3278
4 O5' -19.5650 34.8900 9.8690 O.3 7 EDA7 -0.3092
5 N9 -19.4310 38.0150 10.5210 N.ar 7 EDA7 -0.2879
6 C4 -20.1950 38.7050 11.4430 C.ar 7 EDA7 0.1675
7 N3 -19.8330 39.0530 12.6980 N.ar 7 EDA7 -0.2173
8 C2 -20.7950 39.7250 13.3310 C.ar 7 EDA7 0.1039
9 N1 -22.0180 40.0610 12.8260 N.ar 7 EDA7 -0.2885
10 C6 -22.3730 39.6990 11.5480 C.ar 7 EDA7 0.1681
11 C10 -23.1640 40.7500 13.2720 C.ar 7 EDA7 0.0307
12 C11 -24.0540 40.7310 12.2450 C.ar 7 EDA7 0.0465
13 N6 -23.5790 40.0620 11.1150 N.ar 7 EDA7 -0.2339
14 C5 -21.4040 38.9720 10.8210 C.ar 7 EDA7 0.1505
15 N7 -21.4360 38.4560 9.5220 N.ar 7 EDA7 -0.2303
16 C8 -20.2420 37.9090 9.4010 C.ar 7 EDA7 0.1003
17 C2' -17.9490 36.4070 11.7370 C.3 7 EDA7 0.0213
18 C5' -18.3680 34.6570 9.1140 C.3 7 EDA7 0.0851
19 C4' -17.2610 35.5580 9.6210 C.3 7 EDA7 0.1108
20 O4' -17.6940 36.9230 9.4400 O.3 7 EDA7 -0.3484
21 C1' -18.0700 37.5010 10.6830 C.3 7 EDA7 0.1408
22 C3' -16.9880 35.4100 11.1160 C.3 7 EDA7 0.0877
23 O3' -15.6370 35.7660 11.4270 O.3 7 EDA7 -0.3890
24 H -22.8630 34.3800 10.1050 H 7 EDA7 0.2192
25 H -20.5950 40.0210 14.2990 H 7 EDA7 0.1033
26 H -23.3010 41.1840 14.1980 H 7 EDA7 0.0829
27 H -24.9880 41.1670 12.2950 H 7 EDA7 0.0845
28 H -19.9340 37.4370 8.5370 H 7 EDA7 0.1030
29 H -18.8990 35.9530 11.9260 H 7 EDA7 0.0335
30 H -17.6070 36.7780 12.6810 H 7 EDA7 0.0335
31 H -18.0720 33.6340 9.2230 H 7 EDA7 0.0591
32 H -18.5530 34.8700 8.0820 H 7 EDA7 0.0591
33 H -16.3750 35.2940 9.0820 H 7 EDA7 0.0646
34 H -17.4520 38.3170 10.9930 H 7 EDA7 0.0840
35 H -17.1200 34.4080 11.4680 H 7 EDA7 0.0621
36 H -20.4990 34.8340 7.4060 H 7 EDA7 0.2192
37 H -15.0320 35.1230 11.0250 H 7 EDA7 0.2099
@BOND
1 1 3 1
2 1 4 1
3 1 2 1
4 2 24 1
5 3 36 1
6 4 18 1
7 5 16 ar
8 5 21 1
9 5 6 ar
10 6 14 ar
11 6 7 ar
12 7 8 ar
13 8 9 ar
14 8 25 1
15 9 10 ar
16 9 11 ar
17 10 14 ar
18 10 13 ar
19 11 12 ar
20 11 26 1
21 12 13 ar
22 12 27 1
23 14 15 ar
24 15 16 ar
25 16 28 1
26 17 21 1
27 17 22 1
28 17 29 1
29 17 30 1
30 18 32 1
31 18 31 1
32 18 19 1
33 19 33 1
34 19 20 1
35 19 22 1
36 20 21 1
37 21 34 1
38 22 23 1
39 22 35 1
40 23 37 1

[roccomoretti]

molfile_to_params_polymer.py is a bit of a misnomer -- it's use case is for non-canonical amino acids. It's not set up for nucleic acid polymers.

Unfortunately, I don't think we have a script for automated parameterization of nucleic acids. Your best bet might be to use the regular molfile_to_params.py to generate a params file as if it's a ligand, and then manually edit the params file to adjust for being a polymer, using the files in database/chemical/residue_type_sets/fa_standard/residue_types/nucleic/ as a reference.