Greetings, I have an sdf file (attached) with prepared molecules for docking and want to convert them to pdbqt format by preserving the protons as they are in the sdf. I use the following command line:
obabel -i sdf sample.sdf -o pdbqt -O sample.pdbqt -xh --canonical > However, OpenBabel writes a multi-MODEL pdbqt file (it assumes that the input contains multiple conformations of a single molecule). As such, docking with Smina fails with this error: Parse error on line 1 in file "sample.pdbqt": Unexpected multi-MODEL input. > Use "vina_split" first? > How can I instruct OpenBabel to write a multi-molecule pdbqt file? I am not sure if the flag '--canonical' has any effect. I have heard that sometimes it fixes some random change in the atom order especially in structures with a high number of rotatable bonds and many symmetric groups. I thank you in advance for your help. Thomas PS: although I could use directly the 'sample.sdf' file for docking with Smina, I have noticed differences in the output docking poses when I use pdbqt and sdf, and I am about to submit a bug report. -- ====================================================================== 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, Twitter: tevangelidis <https://twitter.com/tevangelidis>, LinkedIn: Thomas Evangelidis <https://www.linkedin.com/in/thomas-evangelidis-495b45125/> website: https://sites.google.com/site/thomasevangelidishomepage/
sample.sdf
Description: StarMath document
_______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
