For docking purpose, I have drawn my ligand of interest in chemsketch and saved in .mol format. Chemical structure is deformed/changed after converting it into .pdb format with Openbabel. Same problem when tried with Pymol. Kindly, suggest me any good tool for converting into .pdb format without changing chemical structure. Thanks in advance.
Sathish Dorairaj I used to download it in form sdf (3D). the 3D structure will be conserved.
If you want to draw it, try to use Chemdraw.
Hi Sathish Dorairaj,
The same thing happen to me when I used chem sketch for my ligand design but, the structure was deformed after the energy minimization using Hyperchem software so I have open again the same file in .mol format (after minimization) then directly I save it as PDB and the structure stay normal. So the trick is don't move or modify anything after opening the file in the format mol directly save it as PDB format try this.
Discovery studio viewer easy and accurate just open the molecule and then save it as pdb format
Thanks everyone. I used UCSF-Chimera for converting the file types without structural changes. Thanks for your suggestions.
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