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, Sheng On Mon, May 11, 2020 at 1:49 PM Eric Pettersen <pett@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@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 _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users