[Chimera-users] Minimisation error

[Eric Pettersen]

Hi Kyle,
	The MMTK toolkit that Minimize uses does not have support for bromine  
currently.  Nonetheless there are some parameter files for bromine and  
iodine obtained from PyMOMO (http://www.pymomo.de/) that seem  
reasonable that, if you drop them into the right place in your Chimera  
distribution, should get your bromonaphthalene minimization to work.   
For convenience, I've attached the files.  The "right place" is <your  
chimera installation>/lib/python2.7/site-packages/MMTK/Database/Atoms/  
[on Windows or Linux] or Chimera.app/Contents/Frameworks/ 
Python.framework/Versions/2.7/lib/python2.7/site-packages/MMTK/ 
Database/Atoms/ [on Mac].
	Hopefully MMTK will directly support these elements in future releases.

--Eric

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

On Jan 30, 2012, at 12:10 AM, Kyle Morris wrote:

> Hi,
>
> I get a minimisation error - Atom type "Br" is not supported by MMTK  
> - when trying to minimise a PDB that contains a bromonaphthalene  
> covalently bound ligand.
>
> I have read the post by neelagiri.d at gmail.com  and note the Cl  
> substitution does make this work but my Br is part of the molecule  
> and so GAFF/Antechamber should be able to handle it I thought?




-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120130/fb7bed28/attachment.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: br
Type: application/octet-stream
Size: 110 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120130/fb7bed28/attachment.obj>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120130/fb7bed28/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: i
Type: application/octet-stream
Size: 95 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120130/fb7bed28/attachment-0001.obj>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120130/fb7bed28/attachment-0002.html>