[Chimera-users] Question about minimizing molecule with non-standard amino acids

Sheng Zhang shengz4 at uci.edu
Fri May 8 08:00:00 PDT 2020

Dear UCSF Chimera team,

Good morning! I am Sheng Zhang, a graduate student from UC Irvine. First I
would like to thank you for developing this useful tool, UCSF Chimera. I
have a question regarding minimizing molecule with non-standard amino acids.

I modified a linear peptide ligand so it's now a ring containing
non-standard amino acids. When I was trying to minimize the ligand while
fixing its protein partner, I kept getting error messages like "failure
running ANTECHAMBER for residue UNK+THR". The unknown and threonine
residues happen to be the residues that I built and modified. Now they are
no longer standard/intact amino acid residues and I guess that is why
Chimera doesn't like them when trying to minimize the structure.

I wonder is there a way to minimize ligand with non-standard amino acid
groups? Thank you so much for your time and help!

Best wishes,
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