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

Sheng Zhang shengz4 at uci.edu
Mon May 11 18:28:46 PDT 2020

Dear Eric,

Thank you so much for your reply!

I've sent a bug report through Chimera with the reply log file attached. As
I mentioned in the earlier email, the error came from the parts that I
built and modified. I know I must have made some mistakes in the progress,
so your help is greatly appreciated! Please let me know if any further
information is needed. One way I can think of solving this problem is to go
to the original PDB file and change the name of the amino acids that I have
modified, but I may be wrong.

Thank again for your kind help!

Best wishes,

On Mon, May 11, 2020 at 1:49 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:

> 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
> 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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