snugdock ensemble run error

[croshong]

Hi everyone

I am running rosetta for antibody-antigen docking with snugdock + ensemble docking

first I generated the enesmble of antibody and antigen with following flag using relax.linuxgccrelease

1. antibody
   -in:file:s 9eup_HL.LH.pdb
   -nstruct 10
   -relax:fast
   -ex1
   -ex2
   -flip_HNQ
   -no_optH false
   -out:path:all ab_ensembl
   -ignore_zero_occupancy false

2. antigen
   -in:file:s 9eup_HL.A.pdb
   -nstruct 10
   -relax:fast
   -ex1
   -ex2
   -flip_HNQ
   -no_optH false
   -out:path:all ag_ensembl
   -ignore_zero_occupancy false

for antibody the chain order was L(light chain) -> H(Heavy chain)
it runs fine without any error

second I run the prepacking with following flag using docking_prepack_protocol.mpi.linuxgccrelease
-in:file:s 9eup_HLA.LHA_sorted.pdb

-nstruct 1

-partners LH_A

-ensemble1 ab_ensembl.list
-ensemble2 ag_ensembl.list

-ex1
-ex2aro

-out:suffix _ensemble_prepack
-ignore_zero_occupancy false

it also runs fine without any errors
the problem was in third step which is final docking run
I use following flag using snugdock.mpi.linuxgccrelease
-s 9eup_HLA.LHA_sorted_ensemble_prepack_0001.pdb
-antibody:auto_generate_kink_constraint
-antibody:all_atom_mode_kink_constraint
-partners LH_A
-spin
-dock_pert 3 8
-ex1
-ex2aro
-ensemble1 ab_ensembl.list
-ensemble2 ag_ensembl.list
-nstruct 100
-optimization:default_max_cycles 200
-out:path:pdb dock_res

It produces following error
ERROR: Sequence for partner1:
EVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSPEKRLEWVAEISSGGRYIYYSDTVTGRFTISRDNARNILHLEMSSLRSEDTAMYYCARGEVRQRGFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPRENVLTQSPAIMSTSPGEKVTMTCRASSSVGSSYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQFSGYPLTFGSGTKLEMKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE
does not match first member of ensemble1:
ENVLTQSPAIMSTSPGEKVTMTCRASSSVGSSYLHWYQQKSGASPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISSVEAEDAATYYCQQFSGYPLTFGSGTKLEMKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEEVQLVESGGGLVKPGGSLKLSCAASGFTFSSYAMSWVRQSPEKRLEWVAEISSGGRYIYYSDTVTGRFTISRDNARNILHLEMSSLRSEDTAMYYCARGEVRQRGFDYWGQGTTLTVSSAKTTAPSVYPLAPVCGDTTGSSVTLGCLVKGYFPEPVTLTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVTSSTWPSQSITCNVAHPASSTKVDKKIEPR

I found the sequence of first member of ensembl1 which has a suffix *.ppk and input PDB has an sequence which has an chain order Lchain -> Hchain. but the program seems to complain that the chain ordering should be Hchain -> Lchain
but in the snugdock webpage it is written that
'Partners must be ordered in the PDB and partners flag as light chain, heavy chain, and then antigen.'
and in another webpage(https://forum.rosettacommons.org/node/11446)
by swap the order of L chain and H chain, it runs without any error

I'm so confused and how can I solve this problem?

Many thanks for considering this kind of complicated problem

Jong hui

[croshong]

to resolve this problem,
even I know that the input pdb chain order should be Light chain -> Heavy chain -> Antigen chain in snugdock,
I tried to set the chain order of snugdock input pdb as Heavy chain -> Light chain -> antigen chain , it seems to run without any error ( also without above confusing error in snugdock + ensemble)).
when I see the run_log, I could not find anything which seems to be critical error.
I use rosetta3.12
Can I trust the snugdock result with input PDB( Heavy chain -> Light chain -> Antigen chain) ?