mol2 to pdb conversion for docking

Question

[suhas]

I want to convert mol2 file to pdb file. I am using openbabel but while i convert it, the structure of a molecule gets deformed. How can i get a correct pdb structure for docking by autodock vina?

Answer 1

[Petr Ponomarenko]

Molsoft provides free ICM Browser http://www.molsoft.com/icm_browser.html#ibFeatures . It can open .mol2 and save as .pdb

[Petr Ponomarenko]

Also, Molsoft provides software for docking in ICM Pro bundle http://www.molsoft.com/icm_pro.html but it is commercial

[suhas]

IN ICM browser also i m facing same problem. after conversion to pdb the molecule in getting deformed to very strange structure that i can not use in docking. I want 3D structure of 3 molecules. 1) Cyanidin 3-xylosyl galactoside 2)Peonidin 3-xylosyl(feruloylglucosyl)galactoside 3) Peonidin 3-xylosyl(glucosyl)galactoside. Can anyone have pdb files of these or help me to get them. Thank you.

[Petr Ponomarenko]

What do you mean by "getting deformed to very strange structure". Could you please share your the mol2 file as well as pictures of how it looks in your software or how it should look?

[Petr Ponomarenko]

http://autodock.scripps.edu/faqs-help/how-to/how-to-prepare-a-ligand-file-for-autodock4

[Petr Ponomarenko]

if you want to start from "flat 2d molecule" that is not optimized I am not sure. I am using paid version of ICM Pro. There you can extract smiles representation of the 3d structure and create its flat 3d "2d model". http://www.molsoft.com/icmpro/chemistry-convert.html#chemistry-smiles or http://www.molsoft.com/man/icm-commands.html#make-flat but there should be free tools for these too.

If ICM brakes your molecule during mol2->PDB convertion change parameters to read an object from file and do no energy optimization.