[Chimera-users] Help with energy minimization

Eric Pettersen pett at cgl.ucsf.edu
Mon Feb 25 16:21:40 PST 2013

On Feb 22, 2013, at 5:05 PM, Kirsten Reimer wrote:

> Hi there,
> I've been using Chimera for several weeks now and I'm having some trouble with the energy minimization tool. I'm attempting to model a small RNA structure, and I keep getting the same error (using all default settings). To be honest I don't know enough about the program to feel comfortable changing the settings. I've attached the .pdb file that I'm using as well as the error message. Is there some way I could get help with this? Thank you!

Hi Kirsten,
	Your structure already has hydrogens, so when the Dock Prep part of the minimization setup shows up, turn off the "Add hydrogens" check button.  In the "Delete 5' phosphate" dialog, click OK.  I think the minimization then works without any other changes (make sure you are using at least the 1.7 release).
	Your structure seems to get stuck in a high-energy "well" using only steepest-descent steps, so I think you will also have to use a significant amount of conjugate-gradient minimization as well, despite it being quite slow with such a large structure.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

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