Dear all - I'm working with a PDB file with explicit hydrogens where many of the histidines are in protonated form due to crystallization at low pH. Unfortunately, although the additional protons are present in the model for the positively charged histidines, the residues in question are indicated in both the SEQRES and the ATOM records as 3-letter code `HIS` regardless of protonation state (i.e. instead of `HIP` for positively charged, and `HID` or `HIE` for the neutral tautomers).
Are there existing tools available to determine the proper 3-letter residue code for titratable amino acid residues based on which hydrogens are present, and output a corrected PDB file? Thank you in advance for your suggestions. Cheers, Jared Sampson Ph.D. Candidate Columbia University
