[Chimera-users] successive minimizations: can we use a unique protein setup?

Elaine Meng meng at cgl.ucsf.edu
Thu Nov 6 08:53:56 PST 2008

Hi JD,
As you have found, the Minimize Structure tool or minimize command has  
limitations and inconveniences.

If you didn't change the set of atoms (by changing I mean adding atoms  
or swapping a side chain, not just modifying positions such as with  
bond rotation), I believe that when the "prep" dialog appears, you can  
just un-check all of the options (hydrogen addition, etc.) and they  
will not be run again.

However, if you did change the set of atoms (adding, swapping), it is  
necessary to run at least the "add charge" step again because it also  
assigns AMBER atom types to the atoms.  Depending on what you changed,  
it might be necessary to also run "add hydrogens" again; for example,  
if you swap a residue, the new sidechain doesn't include hydrogens yet.

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 6, 2008, at 1:13 AM, Jean Didier Pie Marechal wrote:

> Hi everyone,
> I want to do the following:
> 1. minimize a region of a structure
> 2. change some part of the region by hand (like swap a residue)
> 3. minimize once more.
> and this 2 or three times.
> However, each time I want to minimize I have to pass through the all  
> setup of the protein (add H, hist protonation, and so one).
> Couldn't we keep the information of the first setup and directly fo  
> through the minimization?
> All the best,
> JD

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