I used modeller to generate structure of my membrane protein. But when I
am using that structure in charmm gui to build setup. I am getting error
stating missing residues or error in pdb. How can I rectify it?
I can't help you with the CHARMM GUI, sorry. If that's the literal error
message ("missing residues or error in pdb") it gives you, you'll have
to ask the CHARMM guys to give you something more useful (particularly
if the Modeller PDB output file loads fine in a PDB viewer such as
Chimera or VMD).