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antibody modeling error

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antibody modeling error

Hi all:

      I am going to use antibody.default.linuxgccrelease to make a model for an antibody sequence.  The command I entered is ”antibody.default.linuxgccrelease -fasta mxp335.fasta -antibody::grafting_database  /home/mxp/apps/rosetta/tools/antibody >error1.log“.  I encountered the following error:


core.conformation.Conformation: current variant for 207 CYD
core.conformation.util: [ ERROR ] Residue 10 was disulfide bonded but had no partner
caught exception 

File: src/core/conformation/
[ ERROR ] UtilityExitException


Detailed error log and fasta files are attached to the attachment,can anyone give some advice? 




error1.log23.85 KB
mxp335.fasta_.txt245 bytes
Post Situation: 
Mon, 2019-09-16 18:29


The template 1acy has a cysteine immediately following the H1 region, so when the H1 is grafted from 1acy to your model, that cysteine loses its disulfide bond partner. You can try to exclude 1acy as a template by adding the following command "-antibody:exclude_pdb 1acy", or you can turn off disulfide detection: "-detect_disulf false". Turning off disulfide detection is not recommended because any existing disulfide bonds (e.g. in the framework of the antibody) will be broken.

In any case, I ran the grafting stage with a newer version of Rosetta (command: antibody.default.macosclangrelease -fasta fasta" and did not receive an error. My results are here:, but I will delete these in a week or so.



Fri, 2019-09-20 23:55


“-detect_disulf false” works,but  "-antibody:exclude_pdb 1acy" does not work.  I found a message in the error log is " protocols.antibody.grafting: Not enought templates for region h1 was selected... Adding arbitrary template 1acy",  is it related to this message?

Thank you for your reply!




Mon, 2019-09-23 01:40