I am trying to perform a protein-protein docking using some altered restrains through the GURU mode. 5 of my docking runs have continued for the past week and they seem to be stuck at it0 99%. Is this the normal running time for such complexes or is there any issues?
Thanks for reaching out about this issue, could you please share the run ID?
Hello, thank you for your reply. This has been resolved. I am now facing another issue where I am getting this error in my input PDB file
Error in PDB file.
Issue when parsing the PDB file at line 729 .
Your PDB contains an Unknown residue PDBLine: ATOM 729 N HSD A 50 102.158 130.293 -28.820 1.00 0.00 AP1 N that should be using HETATM record, please check the HADDOCK library for a list of supported modified residues.
Which I am not sure how to resolve
HSD is not an official amino acid name.
Same will apply to HSE. Those should be defined as HIS.
Thank you, so in the PDB files should I change the labels from ATOM to HET or change HSD and HSE to HIS
HSD and HSE to HIS
Thank you, the issue is resolved.