Minimisation error
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? Really appreciate any help. Best wishes, Kyle
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?
On 30 janv. 2012, at 20:34, Eric Pettersen wrote:
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.
They will be in the next release. Konrad. -- --------------------------------------------------------------------- Konrad Hinsen Centre de Biophysique Moléculaire, CNRS Orléans Synchrotron Soleil - Division Expériences Saint Aubin - BP 48 91192 Gif sur Yvette Cedex, France Tel. +33-1 69 35 97 15 E-Mail: research at khinsen dot fastmail dot net ---------------------------------------------------------------------
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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Hi Eric, That's perfect, worked a treat. Thanks for your help. Best wishes, Kyle 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>
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (5)
-
Conrad Huang -
Eric Pettersen -
Konrad Hinsen -
Kyle Morris -
Kyle Morris