[Chimera-users] Solvation question

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 9 13:07:00 PST 2021

Hello Heather,
It may be a quick question but not that quick of an answer...

It sounds like you are using the separate solvation command or tool instead of the Solvation tab in the Molecular Dynamics tool.  Instead, you need to use only the tabs in that tool: first Prep Structure, then Solvation, then Run Parameters. 

The problem is if you solvate separately first, then the Molecular Dynamics tool sees that prepping still needs to be done and calls Dock Prep, which automatically deletes the waters.

I really hope you aren't trying to run this on your capsid model!!  That is waaaay too huge and Chimera's MD calculations way too slow to give any meaningful results.  Please see the gray box with the caveats to this tool in the Molecular Dynamics Simulation documentation:


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

> On Nov 9, 2021, at 12:28 PM, Noriega, Heather via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> Hello,
> I have a quick question. I am running the solvate command before the minimization, equilibrium, and production run in Chimera. I click the start solvate tool and put my water box size and apply. This gives me my box and in the command line it says created...with however many water molecules. I then go run parameters, set up everything. Once I hit run, the water box dissappears. I just want to make sure that the solvation did occur even though the water box dissappears from the screen. Everything else ran smoothly to show simulation. I just want to be certain and have confirmation that the solvation does occur as long as I use apply and do not close out of the window. Thanks in advance for your help. 
> Thank you,
> Heather Noriega

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