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 PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883
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@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
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 why? Thank you, Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883 On Tue, Nov 9, 2021, 4:07 PM Elaine Meng <meng@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@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
Hello Heather, No I do not, sorry. As mentioned in the tool caveats, the tool was developed in large part by another group for small-molecule dynamics, and may not be generally robust for macromolecular calculations. You might need to use a dedicated dynamics package like AMBER or GROMACS instead of Chimera for your application. Elaine
On Nov 9, 2021, at 2:05 PM, Noriega, Heather via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
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 why?
Thank you,
Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883
On Tue, Nov 9, 2021, 4:07 PM Elaine Meng <meng@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@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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It has been my experience that the screen going black means that the simulation failed. Specifically, some of the energies went to infinity and the molecule "exploded". This typically means that some atoms/bonds/angles in your system were not properly parameterized. There should be messages in the Reply Log (Favorites→Reply Log) about missing parameters/radii/masses/charges. Proper parameterization is a pretty advanced topic and requires a bit of expertise. It would also require more control over the simulation than Chimera offers, i.e. using one of the packages that Elaine mentions. --Eric Eric Pettersen UCSF Computer Graphics Lab
On Nov 9, 2021, at 2:37 PM, Elaine Meng via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
Hello Heather, No I do not, sorry.
As mentioned in the tool caveats, the tool was developed in large part by another group for small-molecule dynamics, and may not be generally robust for macromolecular calculations.
You might need to use a dedicated dynamics package like AMBER or GROMACS instead of Chimera for your application. Elaine
On Nov 9, 2021, at 2:05 PM, Noriega, Heather via Chimera-users <chimera-users@cgl.ucsf.edu> wrote:
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 why?
Thank you,
Heather Noriega PhD-Pharmaceutical Science student College of Pharmacy Howard University heather.noriega@bison.howard.edu 520-203-1883
On Tue, Nov 9, 2021, 4:07 PM Elaine Meng <meng@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@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
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
-
Elaine Meng -
Eric Pettersen -
Noriega, Heather