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snugdock run error: Sequence for partner1 does not match first member of ensemble1

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snugdock run error: Sequence for partner1 does not match first member of ensemble1

Hello everyone,

I am trying to use Rosetta for antibody homology modeling and docking.  
The method I used was from article:"Modeling and docking of antibody structures with Rosetta" (
The Rosetta version I used is:  3.13  Release date: Tuesday, June 1, 2021
I performed antibody homology modeling and docking preparation according to the method in the article.  When I run snugDock, the software keeps saying something wrong:  

[ ERROR ] UtilityExitException
ERROR: Sequence for partner1:
 does not match first member of ensemble1:



The code I am executing:

docking_prepack_protocol.mpi.linuxgccrelease  \
    -in:file:s   model-0.relaxed_0168.antibody_antigen_start_new.pdb   \
    -ex1    \
    -ex2    \
    -partners  LH_A  \
    -ensemble1  antibody_ensemble.1.list   \
    -ensemble2  antigen_ensemble.list    \

Based on the log message, I thought there might be a problem with the chain order in my partner1 file or ensemble1. But after checking, I found that the antibody sequence in the ppk file of ensemble1 is fine, the order is: L chain->H chain. in partner1.ppk file, the order of the chain is fine, also L chain->H chain, but the identifier is changed to A and B, which may be handled by the software docking_prepack_protocol.
When I searched for related questions in the forum, I found that the same question was mentioned before by

So I tried to swap the order of L chain and H chain in the partner1.ppk file and changed the chain identifiers to H and L. The rest of the file remained unchanged.
I reran the above command and it works!

However I'm even more confused!

My questions:
1, why does snugdock think my sequence is not match?
2, Can I get normal results with the way I'm running it now? Why I set "-partners LH_A" in the parameter and the sequence order of partner1.ppk is H chain->L chain, but snugdock works well?
3, why the sequence identifier in partner1.ppk be changed to A and B after prepack run?

Post Situation: 
Fri, 2022-03-25 01:21