[Chimera-users] Solvation question

Noriega, Heather heather.noriega at bison.howard.edu
Tue Nov 9 14:05:34 PST 2021

Hello, Elaine,

No, not on my capsid model. I am working on am example monomer. Ok, so in
the Molecular Dynamics Simulation box. I have dock prepped, created my
solvation box, have all the default settings for minimization, equilibrium,
and production. Added a number for the trajectories so they save where I
want them to. Now, the screen goes black around the 8th frame. Do you know

Thank you,

Heather Noriega
PhD-Pharmaceutical Science student
College of Pharmacy
Howard University
heather.noriega at bison.howard.edu

On Tue, Nov 9, 2021, 4:07 PM Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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:
> <https://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/md/md.html>
> Best,
> Elaine
> -----
> 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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