Amber Solvate not responding

[samglaser1997@…]

Hi,

I currently have a double stranded and single stranded DNA segment open in Chimera, and would like to use Amber Solvate with water in order to show that the single strand bases form hydrogen bonds with the solvent. When I click "ok" or "apply" my Solvate settings, I receive a message that Chimera is not responding. Any advice?

Thanks,
Sam

[Eric Pettersen]

Hi Sam,

Since the solvation tool in Amber is designed to be used in conjunction with molecular dynamics, the waters are not placed in any way to optimize hydrogen bonding. For instance, when using a "box" of water, Amber just makes a regular three-dimensional grid of waters and then knocks out the ones in steric conflict with the molecule being solvated. Besides, water will basically always orient to form hydrogen bonds with molecules in solution.
As for the "not responding" problem, my best guess is that you asked for a quite large amount of solvent to be placed, which in turn makes a high demand on system memory and causes swapping -- which will slow Chimera down a lot until it manages to finish the solvation. At any rate, the "not responding" is just that Chimera won't be responding to the mouse or keyboard until the solvation task is finished -- which might be many minutes.

--Eric

Eric Pettersen
UCSF Computer Graphics Lab

[samglaser1997@…]

Hi Eric,

Thanks for your response. I'm writing a lab report on forces that make double stranded DNA more stable than single strand DNA, and am attempting to illustrate the presence of hydrogen bonds in both conformations in order to help emphasize the importance of pi stacking. Thank you for the info regarding how Amber's solvate function works. Do you know if there exists a program I could use that does optimize solvent-to-molecule hydrogen bonds?

Best,
Sam

-----Original Message-----
From: ChimeraX <ChimeraX-bugs-admin@cgl.ucsf.edu> 
Sent: Tuesday, January 5, 2021 1:39 PM
Cc: pett@cgl.ucsf.edu; Glaser, Samuel Abraham <samglaser1997@ku.edu>
Subject: Re: [ChimeraX] #4105: Amber Solvate not responding

#4105: Amber Solvate not responding
----------------------------------------+----------------------------
          Reporter:  samglaser1997@...    |      Owner:  Eric Pettersen
              Type:  defect             |     Status:  closed
          Priority:  normal             |  Milestone:
         Component:  Structure Editing  |    Version:
        Resolution:  nonchimerax        |   Keywords:
        Blocked By:                     |   Blocking:
Notify when closed:                     |   Platform:  all
           Project:  ChimeraX           |
----------------------------------------+----------------------------
Changes (by Eric Pettersen):

 * status:  accepted => closed
 * resolution:   => nonchimerax


Comment:

 Hi Sam,
         Since the solvation tool in Amber is designed to be used in  conjunction with molecular dynamics, the waters are not placed in any way  to optimize hydrogen bonding.  For instance, when using a "box" of water,  Amber just makes a regular three-dimensional grid of waters and then  knocks out the ones in steric conflict with the molecule being solvated.
 Besides, water will basically always orient to form hydrogen bonds with  molecules in solution.
         As for the "not responding" problem, my best guess is that you  asked for a quite large amount of solvent to be placed, which in turn  makes a high demand on system memory and causes swapping -- which will  slow Chimera down a lot until it manages to finish the solvation.  At any  rate, the "not responding" is just that Chimera won't be responding to the  mouse or keyboard until the solvation task is finished -- which might be  many minutes.

 --Eric

         Eric Pettersen
         UCSF Computer Graphics Lab

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[Eric Pettersen]

Hi Sam,

Well, you could minimize the system afterward (Tools→Structure Editing→Minimize), which would tend to move the waters into hydrogen bonding positions. I took a small DNA molecule (1bna) in a box of water and minimized it. Before minimization there were 1192 hydrogen bonds, 4 of which were between the solvent and the DNA, afterward there were 1287 hydrogen bonds, 14 between the solvent and DNA. I only used the default number of steps of minimization, which is somewhat short for this purpose (better suited for just eliminating steric conflicts) so you might want to increase the number of steps -- but you will have to wait awhile for the results (conjugate gradient steps are particularly expensive).

--Eric

[Eric Pettersen]

Also, in the "Dock Prep" dialog of Minimize, make sure to uncheck the "Delete solvent" box!