"I am trying to generate parameters for my ligand when I submit the following command antechamber -i BG6_noH.mol2 -fi mol2 -o BG6_amber.mol2 -fo mol2 -c bcc -pf yes -nc -2 -at gaff2 -j 4
I get the structure which is different from the submitted one.
I wonder which structure I need to use in tleap because the BG6_amber.mol2 is not right I am a little bit confused why it has changed and for which it has generated parameters either for BG6_noH.mol2 or BG6_amber.mol2."
I do not see different structures instead they are exactly the same with just new charges according to the method chosen. Please be more explicit in defining the problem.
Zoran
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Received on Sat Jun 22 2019 - 08:30:02 PDT
