[Chimera-users] Query about energy minimisation

Izzati Mokthar izzati5676 at gmail.com
Sat Oct 17 08:21:04 PDT 2020


I am Izzati. I have a few queries on UCSF Chimera. I need your guide to use
the tools. I have two questions. Below are the questions:

1.I would like to do energy minimisation for protein structure with PDB ID:
2J9F. I click Structure editing > Minimize Structure. To be honest, I
don't know how to set the settings. I used the default setting and a
warning pops up as the attached picture. Do you have any suggestion of
reference that I can refer to, to do the energy minimisation?
[image: 5.png]

2. I need to also do molecular dynamics for my research. May I know
whether I can use chimera to run molecular dynamics as well. If yes, where
can I refer to the tutorials?

Thank you in advance for your response.

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