Maybe try NAOMI from Matthias Rarey's group (https://www.zbh.uni-hamburg.de/forschung/amd/software/naomi.html)
Best, Andrea ---- Prof. Dr. Andrea Volkamer In-silico Toxicology Group<https://physiologie-ccm.charite.de/en/research_at_the_institute/team_volkamer/>, Institute of Physiology, Charité Universitätsmedizin Berlin Campus Mitte: Virchowweg 6, 10117 Berlin Phone: +49 30 - 450 528 504 E-Mail: andrea.volka...@charite.de<mailto:andrea.volka...@charite.de> ________________________________ Von: Thomas Evangelidis [teva...@gmail.com] Gesendet: Montag, 24. September 2018 16:37 An: RDKit Discuss Betreff: [ext] [Rdkit-discuss] online sdf to mol2 converter Greetings, Is anybody aware of a good sdf to mol2 file converter that is not based on OpenBabel? I want to avoid problems like the following, which I currently solve with Maestro. Basically, the problem is with O40 which -according to antechamber from AmberTools- should be sp3 within a non-aromatic pentameric ring, as opposed to OpenBabel which wants it to be sp2 within an aromatic pentameric ring. OpenBabel (AmberTools complain about the valence of O40): @<TRIPOS>MOLECULE BACE7 98 102 0 0 0 SMALL GASTEIGER @<TRIPOS>ATOM 1 C 4.4906 1.0444 -22.8214 C.3 1 LIG1 -0.0624 2 C 4.8922 0.9339 -21.3406 C.3 1 LIG1 -0.0421 3 C 4.7328 -0.5268 -20.8573 C.3 1 LIG1 -0.0504 4 C 5.8712 -1.4883 -21.3104 C.3 1 LIG1 -0.0528 5 C 5.8678 -2.8681 -20.5852 C.3 1 LIG1 -0.0516 6 C 5.7796 -2.6627 -19.0768 C.3 1 LIG1 -0.0371 7 C 6.0082 -3.8328 -18.1147 C.3 1 LIG1 0.0156 8 N 5.0491 -3.7436 -16.9811 N.am 1 LIG1 -0.2907 9 C 5.3910 -3.1904 -15.7259 C.2 1 LIG1 0.2471 10 O 4.9860 -3.7155 -14.6679 O.2 1 LIG1 -0.2700 11 C 6.1926 -1.9707 -15.7016 C.ar 1 LIG1 0.0384 12 C 7.2723 -1.8151 -14.8219 C.ar 1 LIG1 -0.0373 13 C 8.0748 -0.6639 -14.8950 C.ar 1 LIG1 0.0383 14 C 7.7594 0.3295 -15.8386 C.ar 1 LIG1 -0.0373 15 C 6.6529 0.1798 -16.6946 C.ar 1 LIG1 0.0381 16 C 5.9088 -0.9874 -16.6449 C.ar 1 LIG1 -0.0375 17 C 6.3758 1.1928 -17.7374 C.2 1 LIG1 0.2444 18 O 7.3575 1.7202 -18.3089 O.2 1 LIG1 -0.2702 19 N 5.0541 1.4981 -18.2116 N.am 1 LIG1 -0.3060 20 C 4.8315 2.5154 -19.2554 C.3 1 LIG1 0.0508 21 C 4.0479 1.9160 -20.4590 C.3 1 LIG1 -0.0295 22 C 4.1278 3.7525 -18.6377 C.3 1 LIG1 0.0859 23 C 4.9660 4.3781 -17.5041 C.3 1 LIG1 0.0240 24 N 4.2842 5.5876 -17.0101 N.3 1 LIG1 -0.3095 25 C 5.1777 6.6776 -16.6101 C.3 1 LIG1 0.0213 26 C 6.0118 7.1928 -17.7645 C.ar 1 LIG1 -0.0333 27 C 7.4134 7.0911 -17.6697 C.ar 1 LIG1 -0.0573 28 C 8.2301 7.5127 -18.7170 C.ar 1 LIG1 -0.0612 29 C 7.6590 8.0307 -19.8750 C.ar 1 LIG1 -0.0583 30 C 6.2656 8.1500 -19.9835 C.ar 1 LIG1 -0.0445 31 C 5.4430 7.7541 -18.9156 C.ar 1 LIG1 -0.0539 32 C 5.6601 8.6452 -21.2852 C.3 1 LIG1 -0.0215 33 C 4.7533 9.8610 -21.0668 C.3 1 LIG1 -0.0586 34 C 4.9002 7.5146 -21.9875 C.3 1 LIG1 -0.0586 35 O 3.9440 4.7344 -19.6282 O.3 1 LIG1 -0.3887 36 C 9.2604 -0.5139 -14.0265 C.ar 1 LIG1 0.2271 37 N 9.6773 -1.4569 -13.1548 N.ar 1 LIG1 -0.2175 38 C 10.7852 -0.9156 -12.6169 C.ar 1 LIG1 0.0663 39 C 11.0006 0.3233 -13.1739 C.ar 1 LIG1 0.1125 40 O 10.0422 0.5438 -14.0357 O.2 1 LIG1 -0.4436 41 C 3.7184 -4.3654 -17.1815 C.3 1 LIG1 0.0487 42 C 3.6849 -5.7921 -16.6077 C.3 1 LIG1 -0.0422 43 C 2.5948 -3.4594 -16.6885 C.ar 1 LIG1 -0.0273 44 C 2.1036 -2.4496 -17.5372 C.ar 1 LIG1 -0.0568 45 C 1.0992 -1.5797 -17.1055 C.ar 1 LIG1 -0.0614 46 C 0.5629 -1.7113 -15.8244 C.ar 1 LIG1 -0.0617 47 C 1.0304 -2.7139 -14.9731 C.ar 1 LIG1 -0.0614 48 C 2.0402 -3.5825 -15.3976 C.ar 1 LIG1 -0.0568 49 H 5.9644 1.2247 -21.2739 H 1 LIG1 0.0299 50 H 5.7964 2.8799 -19.6624 H 1 LIG1 0.0524 51 H 3.1462 3.4322 -18.2096 H 1 LIG1 0.0624 52 H 3.5467 -4.5027 -18.2736 H 1 LIG1 0.0548 53 H 3.4150 0.7979 -22.9558 H 1 LIG1 0.0232 54 H 5.1004 0.3599 -23.4465 H 1 LIG1 0.0232 55 H 4.6652 2.0788 -23.1866 H 1 LIG1 0.0232 56 H 4.7166 -0.4534 -19.7587 H 1 LIG1 0.0268 57 H 3.7500 -0.9452 -21.1700 H 1 LIG1 0.0268 58 H 5.7965 -1.6618 -22.4043 H 1 LIG1 0.0265 59 H 6.8502 -1.0012 -21.1167 H 1 LIG1 0.0265 60 H 5.0053 -3.4737 -20.9333 H 1 LIG1 0.0266 61 H 6.8042 -3.4123 -20.8288 H 1 LIG1 0.0266 62 H 6.5254 -1.8809 -18.8351 H 1 LIG1 0.0280 63 H 4.7440 -2.3354 -18.8997 H 1 LIG1 0.0280 64 H 7.0562 -3.8126 -17.7420 H 1 LIG1 0.0465 65 H 5.8794 -4.7982 -18.6486 H 1 LIG1 0.0465 66 H 7.5041 -2.6037 -14.1147 H 1 LIG1 0.0633 67 H 8.3749 1.2174 -15.9128 H 1 LIG1 0.0633 68 H 4.9935 -1.0449 -17.2115 H 1 LIG1 0.0633 69 H 4.2242 1.0811 -17.7380 H 1 LIG1 0.1494 70 H 3.1207 1.4242 -20.0987 H 1 LIG1 0.0286 71 H 3.7154 2.7566 -21.1017 H 1 LIG1 0.0286 72 H 5.9766 4.6051 -17.9036 H 1 LIG1 0.0450 73 H 5.0959 3.6528 -16.6730 H 1 LIG1 0.0450 74 H 3.6902 5.3236 -16.1884 H 1 LIG1 0.1223 75 H 4.5586 7.5177 -16.2301 H 1 LIG1 0.0473 76 H 5.8155 6.3352 -15.7648 H 1 LIG1 0.0473 77 H 7.8777 6.6663 -16.7890 H 1 LIG1 0.0621 78 H 9.3069 7.4243 -18.6376 H 1 LIG1 0.0618 79 H 8.3068 8.3297 -20.6899 H 1 LIG1 0.0620 80 H 4.3652 7.8246 -18.9948 H 1 LIG1 0.0623 81 H 6.4721 8.9668 -21.9757 H 1 LIG1 0.0343 82 H 3.8505 9.5898 -20.4774 H 1 LIG1 0.0235 83 H 4.4204 10.2688 -22.0459 H 1 LIG1 0.0235 84 H 5.3112 10.6606 -20.5315 H 1 LIG1 0.0235 85 H 4.0349 7.1733 -21.3729 H 1 LIG1 0.0235 86 H 5.5826 6.6513 -22.1567 H 1 LIG1 0.0235 87 H 4.5216 7.8616 -22.9744 H 1 LIG1 0.0235 88 H 2.9876 4.7176 -19.8960 H 1 LIG1 0.2099 89 H 11.4027 -1.3995 -11.8736 H 1 LIG1 0.0862 90 H 11.8106 1.0050 -12.9533 H 1 LIG1 0.1046 91 H 4.4232 -6.4241 -17.1449 H 1 LIG1 0.0251 92 H 3.9428 -5.8167 -15.5315 H 1 LIG1 0.0251 93 H 2.6779 -6.2381 -16.7493 H 1 LIG1 0.0251 94 H 2.4938 -2.3324 -18.5377 H 1 LIG1 0.0621 95 H 0.7330 -0.8047 -17.7661 H 1 LIG1 0.0618 96 H -0.2211 -1.0413 -15.4952 H 1 LIG1 0.0618 97 H 0.6133 -2.8141 -13.9796 H 1 LIG1 0.0618 98 H 2.3830 -4.3416 -14.7100 H 1 LIG1 0.0621 @<TRIPOS>BOND 1 1 2 1 2 1 53 1 3 1 54 1 4 1 55 1 5 2 49 1 6 2 21 1 7 2 3 1 8 3 4 1 9 3 56 1 10 3 57 1 11 4 5 1 12 4 58 1 13 4 59 1 14 5 6 1 15 5 60 1 16 5 61 1 17 6 7 1 18 6 62 1 19 6 63 1 20 7 8 1 21 7 64 1 22 7 65 1 23 8 9 am 24 8 41 1 25 9 10 2 26 9 11 1 27 11 16 ar 28 11 12 ar 29 12 13 ar 30 12 66 1 31 13 14 ar 32 13 36 1 33 14 15 ar 34 14 67 1 35 15 16 ar 36 15 17 1 37 16 68 1 38 17 18 2 39 17 19 am 40 19 20 1 41 19 69 1 42 20 50 1 43 20 21 1 44 20 22 1 45 21 70 1 46 21 71 1 47 22 51 1 48 22 23 1 49 22 35 1 50 23 24 1 51 23 72 1 52 23 73 1 53 24 25 1 54 24 74 1 55 25 26 1 56 25 75 1 57 25 76 1 58 26 31 ar 59 26 27 ar 60 27 28 ar 61 27 77 1 62 28 29 ar 63 28 78 1 64 29 30 ar 65 29 79 1 66 30 31 ar 67 30 32 1 68 31 80 1 69 32 33 1 70 32 34 1 71 32 81 1 72 33 82 1 73 33 83 1 74 33 84 1 75 34 85 1 76 34 86 1 77 34 87 1 78 35 88 1 79 36 40 ar 80 36 37 ar 81 37 38 ar 82 38 39 ar 83 38 89 1 84 39 40 ar 85 39 90 1 86 41 52 1 87 41 42 1 88 41 43 1 89 42 91 1 90 42 92 1 91 42 93 1 92 43 48 ar 93 43 44 ar 94 44 45 ar 95 44 94 1 96 45 46 ar 97 45 95 1 98 46 47 ar 99 46 96 1 100 47 48 ar 101 47 97 1 102 48 98 1 Meastro (AmberTools consider this correct): @<TRIPOS>MOLECULE BACE7 98 102 1 SMALL USER_CHARGES @<TRIPOS>ATOM 1 C1 4.4906 1.0444 -22.8214 C.3 1 UNK 0.0000 2 C2 4.8922 0.9339 -21.3406 C.3 1 UNK 0.0000 3 C3 4.7328 -0.5268 -20.8573 C.3 1 UNK 0.0000 4 C4 5.8712 -1.4883 -21.3104 C.3 1 UNK 0.0000 5 C5 5.8678 -2.8681 -20.5852 C.3 1 UNK 0.0000 6 C6 5.7796 -2.6627 -19.0768 C.3 1 UNK 0.0000 7 C7 6.0082 -3.8328 -18.1147 C.3 1 UNK 0.0000 8 N8 5.0491 -3.7436 -16.9811 N.am 1 UNK 0.0000 9 C9 5.3910 -3.1904 -15.7259 C.2 1 UNK 0.0000 10 O10 4.9860 -3.7155 -14.6679 O.2 1 UNK 0.0000 11 C11 6.1926 -1.9707 -15.7016 C.ar 1 UNK 0.0000 12 C12 7.2723 -1.8151 -14.8219 C.ar 1 UNK 0.0000 13 C13 8.0748 -0.6639 -14.8950 C.ar 1 UNK 0.0000 14 C14 7.7594 0.3295 -15.8386 C.ar 1 UNK 0.0000 15 C15 6.6529 0.1798 -16.6946 C.ar 1 UNK 0.0000 16 C16 5.9088 -0.9874 -16.6449 C.ar 1 UNK 0.0000 17 C17 6.3758 1.1928 -17.7374 C.2 1 UNK 0.0000 18 O18 7.3575 1.7202 -18.3089 O.2 1 UNK 0.0000 19 N19 5.0541 1.4981 -18.2116 N.am 1 UNK 0.0000 20 C20 4.8315 2.5154 -19.2554 C.3 1 UNK 0.0000 21 C21 4.0479 1.9160 -20.4590 C.3 1 UNK 0.0000 22 C22 4.1278 3.7525 -18.6377 C.3 1 UNK 0.0000 23 C23 4.9660 4.3781 -17.5041 C.3 1 UNK 0.0000 24 N24 4.2842 5.5876 -17.0101 N.3 1 UNK 0.0000 25 C25 5.1777 6.6776 -16.6101 C.3 1 UNK 0.0000 26 C26 6.0118 7.1928 -17.7645 C.ar 1 UNK 0.0000 27 C27 7.4134 7.0911 -17.6697 C.ar 1 UNK 0.0000 28 C28 8.2301 7.5127 -18.7170 C.ar 1 UNK 0.0000 29 C29 7.6590 8.0307 -19.8750 C.ar 1 UNK 0.0000 30 C30 6.2656 8.1500 -19.9835 C.ar 1 UNK 0.0000 31 C31 5.4430 7.7541 -18.9156 C.ar 1 UNK 0.0000 32 C32 5.6601 8.6452 -21.2852 C.3 1 UNK 0.0000 33 C33 4.7533 9.8610 -21.0668 C.3 1 UNK 0.0000 34 C34 4.9002 7.5146 -21.9875 C.3 1 UNK 0.0000 35 O35 3.9440 4.7344 -19.6282 O.3 1 UNK 0.0000 36 C36 9.2604 -0.5139 -14.0265 C.2 1 UNK 0.0000 37 N37 9.6773 -1.4569 -13.1548 N.2 1 UNK 0.0000 38 C38 10.7852 -0.9156 -12.6169 C.2 1 UNK 0.0000 39 C39 11.0006 0.3233 -13.1739 C.2 1 UNK 0.0000 40 O40 10.0422 0.5438 -14.0357 O.3 1 UNK 0.0000 41 C41 3.7184 -4.3654 -17.1815 C.3 1 UNK 0.0000 42 C42 3.6849 -5.7921 -16.6077 C.3 1 UNK 0.0000 43 C43 2.5948 -3.4594 -16.6885 C.ar 1 UNK 0.0000 44 C44 2.1036 -2.4496 -17.5372 C.ar 1 UNK 0.0000 45 C45 1.0992 -1.5797 -17.1055 C.ar 1 UNK 0.0000 46 C46 0.5629 -1.7113 -15.8244 C.ar 1 UNK 0.0000 47 C47 1.0304 -2.7139 -14.9731 C.ar 1 UNK 0.0000 48 C48 2.0402 -3.5825 -15.3976 C.ar 1 UNK 0.0000 49 H49 5.9644 1.2247 -21.2739 H 1 UNK 0.0000 50 H50 5.7964 2.8799 -19.6624 H 1 UNK 0.0000 51 H51 3.1462 3.4322 -18.2096 H 1 UNK 0.0000 52 H52 3.5467 -4.5027 -18.2736 H 1 UNK 0.0000 53 H53 3.4150 0.7979 -22.9558 H 1 UNK 0.0000 54 H54 5.1004 0.3599 -23.4465 H 1 UNK 0.0000 55 H55 4.6652 2.0788 -23.1866 H 1 UNK 0.0000 56 H56 4.7166 -0.4534 -19.7587 H 1 UNK 0.0000 57 H57 3.7500 -0.9452 -21.1700 H 1 UNK 0.0000 58 H58 5.7965 -1.6618 -22.4043 H 1 UNK 0.0000 59 H59 6.8502 -1.0012 -21.1167 H 1 UNK 0.0000 60 H60 5.0053 -3.4737 -20.9333 H 1 UNK 0.0000 61 H61 6.8042 -3.4123 -20.8288 H 1 UNK 0.0000 62 H62 6.5254 -1.8809 -18.8351 H 1 UNK 0.0000 63 H63 4.7440 -2.3354 -18.8997 H 1 UNK 0.0000 64 H64 7.0562 -3.8126 -17.7420 H 1 UNK 0.0000 65 H65 5.8794 -4.7982 -18.6486 H 1 UNK 0.0000 66 H66 7.5041 -2.6037 -14.1147 H 1 UNK 0.0000 67 H67 8.3749 1.2174 -15.9128 H 1 UNK 0.0000 68 H68 4.9935 -1.0449 -17.2115 H 1 UNK 0.0000 69 H69 4.2242 1.0811 -17.7380 H 1 UNK 0.0000 70 H70 3.1207 1.4242 -20.0987 H 1 UNK 0.0000 71 H71 3.7154 2.7566 -21.1017 H 1 UNK 0.0000 72 H72 5.9766 4.6051 -17.9036 H 1 UNK 0.0000 73 H73 5.0959 3.6528 -16.6730 H 1 UNK 0.0000 74 H74 3.6902 5.3236 -16.1884 H 1 UNK 0.0000 75 H75 4.5586 7.5177 -16.2301 H 1 UNK 0.0000 76 H76 5.8155 6.3352 -15.7648 H 1 UNK 0.0000 77 H77 7.8777 6.6663 -16.7890 H 1 UNK 0.0000 78 H78 9.3069 7.4243 -18.6376 H 1 UNK 0.0000 79 H79 8.3068 8.3297 -20.6899 H 1 UNK 0.0000 80 H80 4.3652 7.8246 -18.9948 H 1 UNK 0.0000 81 H81 6.4721 8.9668 -21.9757 H 1 UNK 0.0000 82 H82 3.8505 9.5898 -20.4774 H 1 UNK 0.0000 83 H83 4.4204 10.2688 -22.0459 H 1 UNK 0.0000 84 H84 5.3112 10.6606 -20.5315 H 1 UNK 0.0000 85 H85 4.0349 7.1733 -21.3729 H 1 UNK 0.0000 86 H86 5.5826 6.6513 -22.1567 H 1 UNK 0.0000 87 H87 4.5216 7.8616 -22.9744 H 1 UNK 0.0000 88 H88 2.9876 4.7176 -19.8960 H 1 UNK 0.0000 89 H89 11.4027 -1.3995 -11.8736 H 1 UNK 0.0000 90 H90 11.8106 1.0050 -12.9533 H 1 UNK 0.0000 91 H91 4.4232 -6.4241 -17.1449 H 1 UNK 0.0000 92 H92 3.9428 -5.8167 -15.5315 H 1 UNK 0.0000 93 H93 2.6779 -6.2381 -16.7493 H 1 UNK 0.0000 94 H94 2.4938 -2.3324 -18.5377 H 1 UNK 0.0000 95 H95 0.7330 -0.8047 -17.7661 H 1 UNK 0.0000 96 H96 -0.2211 -1.0413 -15.4952 H 1 UNK 0.0000 97 H97 0.6133 -2.8141 -13.9796 H 1 UNK 0.0000 98 H98 2.3830 -4.3416 -14.7100 H 1 UNK 0.0000 @<TRIPOS>BOND 1 1 2 1 2 1 53 1 3 1 54 1 4 1 55 1 5 2 49 1 6 2 21 1 7 2 3 1 8 3 4 1 9 3 56 1 10 3 57 1 11 4 5 1 12 4 58 1 13 4 59 1 14 5 6 1 15 5 60 1 16 5 61 1 17 6 7 1 18 6 62 1 19 6 63 1 20 7 8 1 21 7 64 1 22 7 65 1 23 8 9 am BACKBONE|DICT|INTERRES 24 8 41 1 25 9 10 2 26 9 11 1 27 11 16 ar 28 11 12 ar 29 12 13 ar 30 12 66 1 31 13 14 ar 32 13 36 1 33 14 15 ar 34 14 67 1 35 15 16 ar 36 15 17 1 37 16 68 1 38 17 18 2 39 17 19 am BACKBONE|DICT|INTERRES 40 19 20 1 41 19 69 1 42 20 50 1 43 20 21 1 44 20 22 1 45 21 70 1 46 21 71 1 47 22 51 1 48 22 23 1 49 22 35 1 50 23 24 1 51 23 72 1 52 23 73 1 53 24 25 1 54 24 74 1 55 25 26 1 56 25 75 1 57 25 76 1 58 26 31 ar 59 26 27 ar 60 27 28 ar 61 27 77 1 62 28 29 ar 63 28 78 1 64 29 30 ar 65 29 79 1 66 30 31 ar 67 30 32 1 68 31 80 1 69 32 33 1 70 32 34 1 71 32 81 1 72 33 82 1 73 33 83 1 74 33 84 1 75 34 85 1 76 34 86 1 77 34 87 1 78 35 88 1 79 36 40 1 80 36 37 2 81 37 38 1 82 38 39 2 83 38 89 1 84 39 40 1 85 39 90 1 86 41 52 1 87 41 42 1 88 41 43 1 89 42 91 1 90 42 92 1 91 42 93 1 92 43 48 ar 93 43 44 ar 94 44 45 ar 95 44 94 1 96 97 45 95 1 98 46 47 ar 99 46 96 1 100 47 48 ar 101 47 97 1 102 48 98 1 @<TRIPOS>SUBSTRUCTURE 1 UNK 1 GROUP 0 **** 0 ROOT -- ====================================================================== Dr Thomas Evangelidis Research Scientist IOCB - Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences<https://www.uochb.cz/web/structure/31.html?lang=en> Prague, Czech Republic & CEITEC - Central European Institute of Technology<https://www.ceitec.eu/> Brno, Czech Republic email: teva...@gmail.com<mailto:teva...@gmail.com> website: https://sites.google.com/site/thomasevangelidishomepage/
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