[Chimera-users] Minimisation error

[Conrad Huang]

Actually, on Windows, the path you want is <your chimera 
installation>/bin/Lib/site-packages/MMTK/Database/Atoms/

Conrad

On 1/30/12 11:34 AM, 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
>> <mailto:chimera-users%40cgl.ucsf.edu?Subject=Re:%20%5BChimera-users%5D%20minimization%20error&In-Reply-To=%3CCANgD7bEi-xXuz%3Dc--MtP-O1-o1ifO8MDeaz89OkTb-JHsSBYbg%40mail.gmail.com%3E>
>> 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?
>
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