Yu Chen's notes
The preparation procedure should be able to handle ATOM/HETATM cards and particularly chain IDs. Chain IDs are very often the source of errors. Also, does the program have the ability to handle residue nos like '28A, 28B"?
What should one pay attention to if the ligand is very big and the binding site is very extended?
What database am I docking again?
docking to AmpC:
1) 1L2S.pdb saved as 1l2s_ampc.pdb.
2) open the pdb in pymol. there are two monomers. decide to use monomer 1 (chain ID 'A') with the bound ligand (name STC, resid 1115)
3) get ampc monomer using shell command
grep " A " 1l2s_ampc.pdb | grep ATOM >! 1l2s_ampc_rec.pdb get rid of the chain id (A in this case) using editor vi (:%s/ A / /g), save and exit(ZZ).
4) get ampc ligand
grep STC 1l2s_ampc.pdb | grep 1115 >! 1l2s_ampc_lig.pdb in vi, get rid of unwanted lines, then change the atom flags :%s/HETATM/ATOM /g