Hi, I use the latest version of openbabel (Open Babel 2.4.1 -- Oct 10 2016 -- 21:27:47) to convert pdbqt file (attached file) to mol format. The command as following：
[cid:image003.png@01D4F492.391D2180] obabel -ipdbqt C:\Users\l\Desktop\ZINC59501033.pdbqt -omol -O C:\Users\l\Desktop\ZINC59501033.mol However, the structure of this molecule is shown below, and is incorrect about the carbon atom selected with red cycle. The valence is five not four. [cid:image005.png@01D4F492.391D2180] However, when I use the web-based convert (openbabel based) to convert the same pdbqt file to mol: http://www.cheminfo.org/Chemistry/Cheminformatics/FormatConverter/index.html# the converted sturcture is correct as following: [cid:image008.png@01D4F492.391D2180] So, please help me to deal with this problem. Any other options do I need to use to do the correct conversion from pdbqt file to mol. Thank you very much. Best Regards. Xin Yan Research Center of Drug Discovery School of Pharmaceutical Science, SUN YAT-SEN UNIVERSITY, High Education Mega Center, Guangzhou, China 510006 Tel: +86-13580418617 QQ: 280878424 E-mail:yanxin_0...@hotmail.com
ZINC59501033.pdbqt
Description: ZINC59501033.pdbqt
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