I try to dock a peptide to a protein containing two chains using “flexpep” protocol.
Is it necessary to rename and renumber the second chain in my protein to have the same chain ID as the first one?
Or there is some option to specify the ID of the two chains as a receptor and the ID of the peptide as a ligand?
By my understanding, you have a three-chain complex, where chains A+B form a protein dimer, and chain C is a peptide you are docking to AB?
The flexpepdock documentation notes the existence of flags -receptor_chain to identify the receptor, and -peptide_chain for the peptide.
I looked through the flexpepdock code, and it strongly suggests to me that it allows _only_ one chain for the receptor.
I found some code that suggests methods for multiple-chain receptors (“updateChainsAndAnchors_fromParamsFile”) but that code is full of comments that suggest it is incomplete and not meant to be used.
I would go ahead and just rename your second protein chain to match the first (you will need to renumber it as well, although not necessarily sequentially). It might work otherwise so you can always give it a shot without that.
I agree with smlewis. just rename the receptor chain to chain A and explicitly supply the peptide chain with the -peptide_chain flag. (or change it too to chain B or whatever)
Just make sure that the receptors chains are first in the input and you are ready to go.
I spoke to Nir and Barak who confirmed that you cannot use multichain receptors – just rename the chains for the receptor to be one chain, and renumber if necessary to prevent the numbers from repeating (i.e. no two instances of the same letter/number combo).