[Chimera-users] Minimisation error

Kyle Morris Kyle.Morris at sussex.ac.uk
Mon Jan 30 14:10:13 PST 2012

Hi Eric,

That's perfect, worked a treat.

Thanks for your help.

Best wishes,
On 30 Jan 2012, at 19:34, Eric Pettersen wrote:

> 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?
> <br>
> <i>
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