Hello, I am new to OB, so please be as simple as possible in your reply. I am having troubles in converting a file containing 105 molecules (either in .smi or .mol format) into 3d .mol format.
Conversion does not end up with the usual message: "105 molecules converted" (as e.g. if I use -gen2d). However, I get the prompt with no error message (meaning the command has been executed) and the output file contains only the first 5 molecules. If I skip the first 5 molecules and start from the sixth using the -f option, the output file is empty, meaning that there is some problem with the .smi/.mol (2d) notation of molecule no. 6. Same thing happens with other molecules in the list (e.g. n. 7, 14). Here is the command I am using: >obabel -ismi input.smi -O output.mol -gen3d (-f 6) And here are the first 10 molecules in SMILES notation: FCCCCCn1cc(c2c1ccnc2)C(=O)Nc1cccc2c1cccc2 O=C(c1nn(c2c1cccc2)CCN1CCCCC1)NC(c1ccccc1)(C)C FCCCCCn1cc(c2c1cccc2)C(=O)N[C@H](C(=O)N)C(C)C FCCCCCn1nc(c2c1cccc2)C(=O)N[C@H](C(=O)N)C(C)C CC([C@@H](C(=O)N)NC(=O)c1cn(c2c1cccc2)Cc1ccccc1)C CC([C@@H](C(=O)N)NC(=O)c1cn(c2c1cccc2)Cc1ccc(cc1)F)C Fc1ccc(cc1)Cn1nc(c2c1c([2H])c([2H])c(c2[2H])[2H])C(=O)N[C@H](C(=O)N)C(C)C CC([C@@H](C(=O)N)NC(=O)c1nn(c2c1cccc2)Cc1ccc(cc1)F)C FCCCCCn1cc(c2c1cccc2)C(=O)N[C@H](C(=O)N)Cc1ccccc1 N#CCCCCn1cc(c2c1nccc2)C(=O)NC(c1ccccc1)(C)C FCCCCCn1nc(c2c1cccc2)C(=O)N[C@H](C(=O)N)Cc1ccccc1 NC(=O)[C@H](C(C)(C)C)NC(=O)c1cn(c2c1cccc2)Cc1ccc(cc1)F OC(=O)CCCn1cc(c2c1cccc2)C(=O)c1cccc2c1cccc2 FCCCCCn1cc(c2c1cccc2)C(=O)NCC1CC1 OCCCCn1c([2H])c(c2c1c([2H])c([2H])c(c2[2H])[2H])C(=O)c1cccc2c1cccc2 Any suggestions? Thanks a lot in advance for your help. Aldo --- Questa e-mail รจ stata controllata per individuare virus con Avast antivirus. https://www.avast.com/antivirus
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