I have been trying to dock a small protein to a lipid_membrane, and much literature has lead me to the HADDOCK webserver. My membrane was prepared using CHAMM GUI. I have tried editing the membrane PDB file as required by making sure all ATOMS are changed to HETATM. However, parsing at line 2 of the lipid_membrane PDB file has continuously failed. Is it true that the webserver surely supports this kind of docking job? If yes, how do I go about it further?
try to keep only the HETATM lines and the final END line, removing all the “junk” in the header
run the file through pdb_tidy and pdb_validate from our pdb-tools
Thank you for your advice on how to tackle the above task. My membrane has POPE, POPG and Cardiolipin (Abbrev. from CHAMM GUI as TMCL). I used pdb_tidy and validated. The pdb_validate returned some errors still but note on line 1. However, I tested by submitting to the webserver, line 1 couldn’t be parsed still, citing line incompatibility.
My questions are,
- Is it right to edit POPE to PE5 as seen from one person in the community who has phospholipid names as “PC5”?
- What other modifications can I do to my pdb file?
- It was mentioned that we should choose “other” or “small molecule” as molecule type, but I don’t see any of such even with expert access. How do I go about that? Thank you very much for your help
try selecting ligand (stands for small molecule)