[Chimera-users] Structure minimization

[Eric Pettersen]

On Jan 15, 2013, at 8:20 AM, Bobo Dang wrote:

> I was trying to use Chimera to minimize a structure I modified and I got the following result. It seems that Chimera was not able to assign the charge to the modified Phe residue (I added one sulfur atom at the beta position of this Phe reidue), do you know how I can fix it?

There are other issues with your structure that you included in your bug report (and I will be getting back to you on those) but one thing I can say immediately and that is of general relevance is that if you modify a standard residue then you have to change the residue name.  Chimera assigns atom types and charges to standard residues (i.e. a residue with a standard name) by using a template -- and such atom types and charges will not be correct if the residue has been modified.  Furthermore, the underlying MMTK minimization code also uses templates for standard residues and expects all the normal atoms and bonds to exist.

--Eric

                        Eric Pettersen
                        UCSF Computer Graphics Lab
                        http://www.cgl.ucsf.edu


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