[chimerax-users] How to complete docking with ChimeraX

[Elaine Meng]

Although it's not the same as minimization, if the structure contains only standard residues (amino acids) and water, if you add hydrogens you can then do a little jiggling/relaxation using the "tug" command with zero force (unless you want to constrain any atoms to current positions) and low temperature.  For example, to reduce clashes between nonhydrogen atoms:

open 2gbp
delete ligand
addh
display
clashes ~H restrict both
tug @ca to @ca force 0 temp 10 steps 100 frames 50
clashes ~H restrict both

See tug:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/tug.html>
...and clashes:
<https://rbvi.ucsf.edu/chimerax/docs/user/commands/clashes.html>

For a more general minimization tool, including parametrization of nonstandard residues like ligands (which is not very simple), we are working on adding a procedure in ChimeraX similar to that in Chimera.

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

> On Jul 11, 2022, at 8:02 AM, 刘 金鑫 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
> 
> Thanks, What a pity. I hope to add some simple functions, such as protein energy minimize.
> Best Regards,
> Jinxin Liu
> Wuxi AppTec
> 
> Phone: +86-18811123206
> WeChat: ljx_19901018
> E-mail: liu_jinxin at wuxiapptec.com or jinxinliu90 at icloud.com
> 
>> 在 2022年7月11日，22:50，Elaine Meng <meng at cgl.ucsf.edu> 写道：
>> 
>> Hi Jinxin,
>> Sorry, ChimeraX does not have a tool to run docking calculations. We currently recommend using the docking program directly (Autodock Vina, DOCK, or others), not from inside Chimera/ChimeraX.  After you get the output docking results file, you can open and analyze it using Chimera's ViewDock tool or ChimeraX's ViewDockX tool.
>> 
>> ViewDockX:
>> <https://rbvi.ucsf.edu/chimerax/docs/user/tools/viewdockx.html>
>> 
>> The Chimera tool "Autodock Vina" is not recommended for most research purposes anyway, because it does not allow very much sampling or searching a ligand database -- see the warning in the bottom part of the gray box on the help page:
>> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/vina/vina.html>
>> 
>> I hope this helps,
>> Elaine
>> -----
>> Elaine C. Meng, Ph.D.                       
>> UCSF Chimera(X) team
>> Department of Pharmaceutical Chemistry
>> University of California, San Francisco
>> 
>> 
>>> On Jul 11, 2022, at 2:29 AM, 刘 金鑫 via ChimeraX-users <chimerax-users at cgl.ucsf.edu> wrote:
>>> 
>>> Dears,
>>> I want to use ChimeraX to dock. The old version can combine with Vina. But I cann't to find the menu in the ChimeraX.
>>> Would it be possible?
>>> Best regards
>>> Jinxin
>>