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C-termini remodelling of dimeric structure removes second chain

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C-termini remodelling of dimeric structure removes second chain

Dear Rosetta Community,

I am trying to remodel a short C-terminal loop into  a docked dimeric structure consisting of 2 identical proteins and while the modeling itself worked, the output contains only the first protein.  The flags I used are the following:
-in:file:s bestp1.pdb
-remodel:blueprint c-term.remodel
-no_optH false
-remodel:num_trajectory 1

( blueprint and pdb file are attached )
Unfortunatly the missing loop resides in the binding cleft between the proteins so that adding the second protein after remodeling results in clashes as the loop overlapps with residues from the second protein. So just model the first protein alone and then merge them is not an option for me. 
I have tried multiple things including merging the dimer, removing the chain identifiers (as hinted in: )  and switching the chains, but none of it worked.
Strangely enough doing the same procedure with an N-terminal loop works fine so I really do not get what the underlying issue might be.
I am using rosetta_bin_linux_2020.37.61417_bundle by the way

Thanks in advance,


Post Situation: 
Wed, 2021-10-13 06:23