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

Eric Pettersen pett at cgl.ucsf.edu
Mon May 11 13:49:37 PDT 2020

Hi Sheng,
	Chimera can definitely handle minimizing non-standard residues.  There are various possibilities as to why it failed with your particular residue, but I would need more than the “failure running ANTECHAMBER” message to diagnose the problem.  Could you repeat what you did and after you get the failure please use Help→Report A Bug to send a bug report to us?  That will include the full contents of the Reply Log, which is what I need to see.  Thanks.


	Eric Pettersen
	UCSF Computer Graphics Lab

> On May 8, 2020, at 8:00 AM, Sheng Zhang <shengz4 at uci.edu> wrote:
> 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,
> Sheng
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