I have a complex, a receptor, and a ligand. The ligand is a short peptide. I want to make a model of the complex using a modeler program. How should I make the aln.file?
I used the online territorial of the modeler which have an example. I followed the example but didn't get any result. My aln file is attached. Please help.
Best.
Najme,
As I understood, U have a complex with PDB coordinates as u mentioned in e1e2-2 file. If you have like this, u can model. But if you have receptor and ligand in different structures like in e1e2 file, say different pdb id, its not complex. They have different crystallographic symmetries.
So you need to reframe your question clearly.
If e1e2-2 is the case, you can model it without issues. Please verify and depict the residue numbers clearly. You can remove everything except the protein and ligand, which is called preprocessing the pdb file then use it as template.
Are you getting any error from modeller or you could model complex but not as expected.
Please post the question precise.
Hope this might help you.
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