Which program can i use to complete the structure of a pdb with missing atoms?, i got several tools online like PDB2PDR, and what i found some are commercial tools, but all i want to do is to complete it.
Please let me know some free tool.
Chimera works here pretty well (as are many other programs). There is a good tutorial on completing the structure of a protein available for that program here: http://dock.compbio.ucsf.edu/DOCK_6/tutorials/struct_prep/prepping_molecules.htm (it's actually for preparing a protein for docking using DOCK, but it also works in a general case of missing some atoms in residues).
You can use psfgen, it's free. You would need to have a topology file to execute it. Standard topology files you can download from CHARMM.
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