[Chimera-users] A problem on minmize structure

[Elaine Meng]

Dear Xinxin Zhu,
The process for automatically assigning parameters and charges in Chimera is meant be simple and easy, but it does not work for everything.  As it says in the help page,
<https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html>

"Note that Antechamber/GAFF are meant to handle most small organic molecules, but not metal complexes, inorganic compounds, or unstable species such as radicals, and may not work well on highly charged molecules." 

NADPH, for example, is a highly charged molecule and the charge calculation may fail.  You could try using the simpler "Gasteiger" charge calculation method and see if that works. If that doesn't work, sorry, you cannot minimize your enzyme + NADPH in Chimera.

Best,
Elaine
-----
Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Aug 27, 2022, at 2:03 AM, 朱鑫鑫 via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Hello everyone
> 
> 
> 
>     I want to conduct a minimize structure using a protein complex model, but a error appears during this process. It reminds me to assign the hydrogen geometry info to NADP, and I click these options, but, it next will report a error. And I DONT know how to sovle this problem. I hope some suggestions I will obtain. Thank you very much.
> 
> 
> 
> Xinxin  Zhu 
> 
> 27/8/2022
> 
> <1661590697981.png>
> 
> <1661590882786.png>
> 
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