I’m trying to dock a protein to a glycoprotein. As part of this in my glycoprotein, I have chain A with atoms numbered 1-9192. After that for the relevant glycan residues, they’re part of HETATM labelled with chain G. For example:
HETATM 9193 C1 NAG G2000 115.116 143.737 183.737 0.00 0.00 C
HETATM 9194 C2 NAG G2000 114.443 144.217 185.063 0.00 0.00 C
HETATM 9195 C3 NAG G2000 113.283 145.209 184.736 0.00 0.00 C
HETATM 9196 C4 NAG G2000 113.757 146.357 183.823 0.00 0.00 C
HETATM 9197 C5 NAG G2000 114.434 145.798 182.541 0.00 0.00 C
I then tried to use the webserver to dock the glycoprotein and my other protein. However, I’m getting the error:
Error: Error in PDB file. Your PDB contains multiple residues with number 2000 in chain G or duplicated atom names.
I don’t think it’s recognizing that I have different atoms as part of the same residue for instance 2000 in this case. I checked a bunch of online glycoproteins from the PDB site and the sugar tree atoms should be in the same format. Am I missing something or is there another workaround to this error? Do I just need to label every line with a different residue number? Thanks in advance!