rnakb_utils ======================== A lib to run RNAkb (http://csb.stanford.edu/rna) (previous Gromacs) utils. A module with different functions needed for Gromacs/RNAkb merriage. Authors: Marcin Magnus, Albert Bogdanowicz Step: (1) prepare groups and then (2) mdp score file (auto) Features: - `G` will be changed into `RG` - `RG3` will be changed into `RG` and TER are kept (`3nt_edited.pdb -> 3nt_edited_rnakb_ready.pdb`) - gromacs ready has `RG3` (`gromacs_ready.pdb`) - if nt is missing, then groups and mdp will be made accordingly WARNING: all-atoms still does not work because for all groups for all-atoms causes `Error: aa is off because of "a line longer than 4095 characters"` .. example (`3nt_edited_rnakb_ready.pdb`): ATOM 1 O5' RU A 7 20.386 15.427 27.178 0.50 21.61 O ATOM 2 C5' RU A 7 21.339 16.437 27.476 0.50 21.61 C ATOM 3 C4' RU A 7 20.788 17.269 28.593 0.50 21.61 C ATOM 4 O4' RU A 7 21.887 17.703 29.427 0.50 21.61 O ATOM 5 C3' RU A 7 20.044 18.519 28.142 0.50 21.61 C ATOM 6 O3' RU A 7 18.630 18.402 28.230 0.50 21.61 O ATOM 7 C2' RU A 7 20.531 19.629 29.069 0.50 21.61 C ATOM 8 O2' RU A 7 19.599 19.988 30.066 0.50 21.61 O ATOM 9 C1' RU A 7 21.778 19.073 29.737 0.50 21.61 C ATOM 10 N1 RU A 7 21.982 20.165 29.489 0.50 21.16 N ATOM 11 C2 RU A 7 21.654 21.439 29.911 0.50 21.16 C ATOM 12 O2 RU A 7 20.786 21.663 30.736 0.50 21.16 O ATOM 13 N3 RU A 7 22.381 22.449 29.329 0.50 21.16 N ATOM 14 C4 RU A 7 23.381 22.315 28.389 0.50 21.16 C ATOM 15 O4 RU A 7 23.946 23.319 27.959 0.50 21.16 O ATOM 16 C5 RU A 7 23.663 20.962 28.001 0.50 21.16 C ATOM 17 C6 RU A 7 22.970 19.961 28.551 0.50 21.16 C ATOM 18 P RG A 8 17.910 18.422 26.467 1.00 19.94 P ATOM 19 OP1 RG A 8 16.664 17.621 26.608 1.00 19.94 O ATOM 20 OP2 RG A 8 18.611 18.475 25.153 1.00 19.94 O ATOM 21 O5' RG A 8 17.621 19.921 26.924 1.00 19.94 O ATOM 22 C5' RG A 8 16.785 20.193 28.035 1.00 19.94 C ATOM 23 C4' RG A 8 16.850 21.657 28.391 1.00 19.94 C ATOM 24 O4' RG A 8 18.212 22.012 28.753 1.00 19.94 O ATOM 25 C3' RG A 8 16.503 22.611 27.266 1.00 19.94 C ATOM 26 O3' RG A 8 15.096 22.790 27.179 1.00 19.94 O ATOM 27 C2' RG A 8 17.213 23.882 27.705 1.00 19.94 C ATOM 28 O2' RG A 8 16.507 24.581 28.705 1.00 19.94 O ATOM 29 C1' RG A 8 18.509 23.314 28.282 1.00 19.94 C ATOM 30 N9 RG A 8 19.551 23.159 27.289 1.00 18.28 N ATOM 31 C8 RG A 8 20.143 22.006 26.833 1.00 18.28 C ATOM 32 N7 RG A 8 21.143 22.225 26.023 1.00 18.28 N ATOM 33 C5 RG A 8 21.219 23.603 25.938 1.00 18.28 C ATOM 34 C6 RG A 8 22.106 24.435 25.207 1.00 18.28 C ATOM 35 O6 RG A 8 23.034 24.098 24.462 1.00 18.28 O ATOM 36 N1 RG A 8 21.833 25.786 25.403 1.00 18.28 N ATOM 37 C2 RG A 8 20.830 26.275 26.206 1.00 18.28 C ATOM 38 N2 RG A 8 20.722 27.609 26.271 1.00 18.28 N ATOM 39 N3 RG A 8 19.998 25.515 26.891 1.00 18.28 N ATOM 40 C4 RG A 8 20.244 24.199 26.714 1.00 18.28 C TER ATOM 41 P RG B 9 27.751 32.185 24.626 0.50 20.93 P ATOM 42 OP1 RG B 9 28.381 33.516 24.464 0.50 20.93 O ATOM 43 OP2 RG B 9 28.555 30.940 24.632 0.50 20.93 O ATOM 44 O5' RG B 9 26.947 32.163 26.015 0.50 20.93 O ATOM 45 C5' RG B 9 25.668 32.799 26.021 0.50 20.93 C ATOM 46 C4' RG B 9 24.887 32.643 27.310 0.50 20.93 C ATOM 47 O4' RG B 9 23.917 31.568 27.169 0.50 20.93 O ATOM 48 C3' RG B 9 25.706 32.357 28.567 0.50 20.93 C ATOM 49 O3' RG B 9 25.420 33.282 29.611 0.50 20.93 O ATOM 50 C2' RG B 9 25.294 30.954 29.001 0.50 20.93 C ATOM 51 O2' RG B 9 25.057 30.821 30.385 0.50 20.93 O ATOM 52 C1' RG B 9 24.020 30.643 28.230 0.50 20.93 C ATOM 53 N9 RG B 9 24.159 29.584 27.812 0.50 20.22 N ATOM 54 C8 RG B 9 25.187 29.306 26.944 0.50 20.22 C ATOM 55 N7 RG B 9 25.369 28.028 26.754 0.50 20.22 N ATOM 56 C5 RG B 9 24.405 27.423 27.539 0.50 20.22 C ATOM 57 C6 RG B 9 24.110 26.051 27.746 0.50 20.22 C ATOM 58 O6 RG B 9 24.669 25.064 27.251 0.50 20.22 O ATOM 59 N1 RG B 9 23.047 25.874 28.628 0.50 20.22 N ATOM 60 C2 RG B 9 22.354 26.894 29.235 0.50 20.22 C ATOM 61 N2 RG B 9 21.359 26.526 30.053 0.50 20.22 N ATOM 62 N3 RG B 9 22.617 28.173 29.053 0.50 20.22 N ATOM 63 C4 RG B 9 23.646 28.369 28.201 0.50 20.22 C TER END