[Chimera-users] [Chimera] #12778: failure assigning charges to FAD (was: Chimera bug report submission)

Eric Pettersen pett at cgl.ucsf.edu
Fri Jan 17 11:30:08 PST 2014

Hi Will,
	The underlying program that Chimera uses to compute charges, antechamber/sqm from AmberTools, frequently fails for molecules with regions of concentrated negative charge, such as the central phosphate connector of FAD.  It not really something I can do much about.  Nonetheless, the failure not only depends on the charge density but also on the specific atomic geometry.  So for instance, I can compute the charges for the FAD in 4kpu, though it does take a long time (about 10 minutes).  This means that there is kind of a work around.  Compute the charges in a structure that works and then transfer them to your structure.  You do this by bringing up the Render by Attribute tool after successfully computing charges and using it's File->Save Attributes menu entry to save the charges to a file.  You should select the FAD and then restrict the save to selected atoms.  Edit the resulting file and change the residue name and chain ID (in this case 401.A) to FAD so that it can be applied to all FADs in your structure.  Then in the Chimera with your structure open, read in the charge-attribute file with the Define Attributes tool.  To save you a lot of the effort here, I've attached the edited charge-attribute file I saved from 4kpu.


                        Eric Pettersen
                        UCSF Computer Graphics Lab

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140117/a8f1f778/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: charges
Type: application/octet-stream
Size: 1503 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140117/a8f1f778/attachment.obj>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20140117/a8f1f778/attachment-0001.html>

More information about the Chimera-users mailing list