Re: [Rdkit-discuss] [ext] online sdf to mol2 converter
The joy of aromaticity models. Via Noel if you're running the (dev/master) version of OpenBabel you can specify *-aa* to take the aromaticity from the input. For example >obabel -:o11 -omol2 -aa > @MOLECULE > * > 5 5 0 0 0 > SMALL > GASTEIGER > @ATOM > 1 O 0.0.0. O.2 1 UNL1 -0.4473 > 2 C 0.0.0. C.ar <http://c.ar/>1 > UNL10.1798 > 3 C 0.0.0. C.ar <http://c.ar/>1 > UNL10.0439 > 4 C 0.0.0. C.ar <http://c.ar/>1 > UNL10.0439 > 5 C 0.0.0. C.ar <http://c.ar/>1 > UNL10.1798 > @BOND > 1 1 2 ar > 2 2 3 ar > 3 3 4 ar > 4 4 5 ar > 5 1 5 ar > 1 molecule converted > >obabel -:O1C=CC=C1 -omol2 -aa > @MOLECULE > * > 5 5 0 0 0 > SMALL > GASTEIGER > @ATOM > 1 O 0.0.0. O.2 1 UNL1 -0.4473 > 2 C 0.0.0. C.2 1 UNL10.1798 > 3 C 0.0.0. C.2 1 UNL10.0439 > 4 C 0.0.0. C.2 1 UNL10.0439 > 5 C 0.0.0. C.2 1 UNL10.1798 > @BOND > 1 1 21 > 2 2 32 > 3 3 41 > 4 4 52 > 5 1 51 > 1 molecule converted However Mol2 support is still not likely to be great. On Mon, 24 Sep 2018 at 16:14, Volkamer, Andrea wrote: > 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 > -- > *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): > > @MOLECULE > BACE7 > 98 102 0 0 0 > SMALL > GASTEIGER > > @ATOM > 1 C 4.49061.0444 -22.8214 C.3 1 LIG1 > -0.0624 > 2 C 4.89220.9339 -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.am1 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.ar1 LIG1 > 0.0384 > 12 C 7.2723 -1.8151 -14.8219 C.ar1 LIG1 > -0.0373 > 13 C 8.0748 -0.6639 -14.8950 C.ar1 LIG1 > 0.0383 > 14 C 7.75940.3295 -15.8386 C.ar1 LIG1 > -0.0373 > 15 C 6.65290.1798 -16.6946 C.ar1 LIG1 > 0.0381 > 16 C 5.9088 -0.9874 -16.6449 C.ar1 LIG1 > -0.0375 > 17 C 6.37581.1928 -17.7374 C.2 1 LIG1 > 0.2444 > 18 O 7.35751.7202 -18.3089 O.2 1 LIG1 > -0.2702 > 19 N 5.05411.4981 -18.2116 N.am1 LIG1 > -0.3060 > 20 C 4.83152.5154 -19.2554 C.3 1 LIG1 > 0.0508 > 21 C 4.04791.9160 -20.4590 C.3 1 LIG1 > -0.0295 > 22 C 4.12783.7525 -18.6377 C.3 1 LIG1 > 0.0859 > 23 C 4.96604.3781 -17.5041 C.3 1 LIG
Re: [Rdkit-discuss] [ext] online sdf to mol2 converter
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): @MOLECULE BACE7 98 102 0 0 0 SMALL GASTEIGER @ATOM 1 C 4.49061.0444 -22.8214 C.3 1 LIG1 -0.0624 2 C 4.89220.9339 -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 LIG10.0156 8 N 5.0491 -3.7436 -16.9811 N.am1 LIG1 -0.2907 9 C 5.3910 -3.1904 -15.7259 C.2 1 LIG10.2471 10 O 4.9860 -3.7155 -14.6679 O.2 1 LIG1 -0.2700 11 C 6.1926 -1.9707 -15.7016 C.ar1 LIG10.0384 12 C 7.2723 -1.8151 -14.8219 C.ar1 LIG1 -0.0373 13 C 8.0748 -0.6639 -14.8950 C.ar1 LIG10.0383 14 C 7.75940.3295 -15.8386 C.ar1 LIG1 -0.0373 15 C 6.65290.1798 -16.6946 C.ar1 LIG10.0381 16 C 5.9088 -0.9874 -16.6449 C.ar1 LIG1 -0.0375 17 C 6.37581.1928 -17.7374 C.2 1 LIG10.2444 18 O 7.35751.7202 -18.3089 O.2 1 LIG1 -0.2702 19 N 5.05411.4981 -18.2116 N.am1 LIG1 -0.3060 20 C 4.83152.5154 -19.2554 C.3 1 LIG10.0508 21 C 4.04791.9160 -20.4590 C.3 1 LIG1 -0.0295 22 C 4.12783.7525 -18.6377 C.3 1 LIG10.0859 23 C 4.96604.3781 -17.5041 C.3 1 LIG10.0240 24 N 4.28425.5876 -17.0101 N.3 1 LIG1 -0.3095 25 C 5.17776.6776 -16.6101 C.3 1 LIG10.0213 26 C 6.01187.1928 -17.7645 C.ar1 LIG1 -0.0333 27 C 7.41347.0911 -17.6697 C.ar1 LIG1 -0.0573 28 C 8.23017.5127 -18.7170 C.ar1 LIG1 -0.0612 29 C 7.65908.0307 -19.8750 C.ar1 LIG1 -0.0583 30 C 6.26568.1500 -19.9835 C.ar1 LIG1 -0.0445 31 C 5.44307.7541 -18.9156 C.ar1 LIG1 -0.0539 32 C 5.66018.6452 -21.2852 C.3 1 LIG1 -0.0215 33 C 4.75339.8610 -21.0668 C.3 1 LIG1 -0.0586 34 C 4.90027.5146 -21.9875 C.3 1 LIG1 -0.0586 35 O 3.94404.7344 -19.6282 O.3 1 LIG1 -0.3887 36 C 9.2604 -0.5139 -14.0265 C.ar1 LIG10.2271 37 N 9.6773 -1.4569 -13.1548 N.ar1 LIG1 -0.2175 38 C 10.7852 -0.9156 -12.6169 C.ar1 LIG10.0663 39 C 11.00060.3233 -13.1739 C.ar1 LIG10.1125 40 O 10.04220.5438 -14.0357 O.2 1 LIG1 -0.4436 41 C 3.7184 -4.3654 -17.1815 C.3 1 LIG10.0487 42 C 3.6849 -5.7921 -16.6077 C.3 1 LIG1 -0.0422 43 C 2.5948 -3.4594 -16.6885 C.ar1 LIG1 -0.0273 44 C 2.1036 -2.4496 -17.5372 C.ar1 LIG1 -0.0568 45 C 1.0992 -1.5797 -17.1055 C.ar1 LIG1 -0.0614 46 C 0.5629 -1.7113 -15.8244 C.ar1 LIG1 -0.0617 47 C 1.0304 -2.7139 -14.9731 C.ar1 LIG1 -0.0614 48 C 2.0402 -3.5825 -15.3976 C.ar1 LIG1 -0.0568 49 H 5.96441.2247 -21.2739 H 1 LIG10.0299 50 H