Dear researchers,
I am not obtaining correct structure in output file .mol2 or .pdb from mol file in Open Babel.
I am drawing structure in Chemdraw and saving it as .cdx file. Then I save it as a .mol file and then try to convert it to .mol2 or .pdb file using Open Babel. But after opening it in Chimera, I am seeing that the structure is tampered and disturbed. Why it must be happening so?
Can anybody suggest how to resolve this issue. Even a different tool to obtain correct .mol2 or .pdb file is welcome. Thanks in advance!