Dear all,
I am trying to modeling a camelid antibody with the sequence (nb.fasta) as following:
$cat nb.fasta
>heavy
QVQLQESGGGLVQAGGSLRLSCAASGTIFETEGMGWYRQAPGKEREFVATIGGGSITYYADSVKGRFTISRDNAKNTVYLQMNSLKPEDTAVYYCAVIAFTEHKYSYWGQGTQVTVSSLE
I use antibody.linuxgccrelease to model it:
mpirun -np 6 antibody.mpi.linuxgccrelease -fasta nb.fasta -vhh_only | tee grafting.log
I got the following error information:
core.conformation.util: (0) [ ERROR ] Residue 7 was disulfide bonded but had no partner
core.conformation.util: (6) [ ERROR ] Residue 7 was disulfide bonded but had no partner
core.conformation.util: (1) [ ERROR ] Residue 7 was disulfide bonded but had no partner
core.conformation.util: (2) [ ERROR ] Residue 7 was disulfide bonded but had no partner
core.conformation.util: (3) [ ERROR ] Residue 7 was disulfide bonded but had no partner
core.conformation.util: (7) [ ERROR ] Residue 7 was disulfide bonded but had no partner
core.conformation.util: (8) [ ERROR ] Residue 7 was disulfide bonded but had no partner
core.conformation.util: (4) [ ERROR ] Residue 7 was disulfide bonded but had no partner
core.conformation.util: (10) [ ERROR ] Residue 7 was disulfide bonded but had no partner
core.conformation.util: (9) [ ERROR ] Residue 7 was disulfide bonded but had no partner
core.conformation.util: (11) [ ERROR ] Residue 7 was disulfide bonded but had no partner
core.conformation.util: (5) [ ERROR ] Residue 7 was disulfide bonded but had no partner
I don't understand this error: residue 7 is Ser (S) (cyan), how can it be disulfide bonded? The two Cys (C) for the disulfide bond are present (red) in the sequene. So what is the real problem with this sequence?
I will appreciate any help. Thank you very much!