Hi Ravi,

You should open your .pdb file by a text editor, and delete the coordinates of ornithine, HETATOMS, ions, and ligand.

For file format conversion, try Open Babel.

Yoshinobu Ishikawa Thank you for your help.

If you are new in this area, use Discovery Studio Clint (free) to build your oligomer and save the file in .pdb format.

For preparing .pdb files for docking

you can use discovery studio client (free) or pymol (free academic license)

First of all look for name of chain of ur interest in ur downloaded pdb structure.

Delete all the chains except oligomer chain. Save it as .pdb

Nayim Sepay Thank you, will surely use this one.