[Chimera-users] Error while using minimize

Elaine Meng meng at cgl.ucsf.edu
Mon Feb 12 09:52:11 PST 2018

Hello Andres,
The error message says that there are nonstandard hydrogen names.  If I restore your session,  then just delete the hydrogens, command:

delete H

 ...and then minimize (minimization prep will add them back),  it works for me.

By the way, you can easily mutate residues in Chimera, see command “swapaa”


I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 9, 2018, at 5:50 PM, Andres Benitez <andresbenitez at gmail.com> wrote:
> Hello,
> I am trying to use minimize to resolve side chain positions which were mutated using pymol. The file is saved as a pdb, but I am getting errors when I try to use the minimize function. I am wondering if the error is because the structure has some loops removed, or if there is something else going on. I've attached the chimera session file and a text file with the errors I am getting.
> Thanks,
> Andres Benitez
> <error_minimize.txt><DRD2_mutated.py>

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