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Error in snugdock application

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Error in snugdock application


 Hi all

 Recently  I;m involved in antibody related project

 While I'm running snugdock application with my antibody( H chain: Lchain) and antigen complex

 I got following error :

 Can't find residue type 'VRT' in type set of mode fa_standard

 In my PDB , only standard amino acid residues are there.

 and I think VRT means something like virtual related object.

 I don't know why this kind of error occur

 Attached file is my pdb file with this error

 Any kind of comments would be welcomed


test.pdb463.79 KB
Post Situation: 
Tue, 2024-05-28 00:59

VRT is indeed a "virtual" residue (used for placeholder purposes) and should be part of the most recent residue type sets. I'm not sure why you're having issues.

My one guess is that you have options (like `-restore_pre_talaris_2013_behavior`) which results in using a residue type set which does not have a VRT residue. I would check your command line for any such mode flags, and see if you can remove them.


P.S. We're updating the site, and as part of that we're moving the forums to Github Discussions.

If you have additional questions or are still having issues, please feel free to open up a thread over there.

Thu, 2024-06-20 13:45