I am trying to assign charges to a compound that contains a sulfone group. The charge assignment depends upon how I name the atoms. The atom assignment for the oxygens that are part of the sulfone group and the sulfur itself vary depending upon how they are named. How should I name them so that they are handled correctly? Barb Truitt PS - I receive the Chimera list emails, but my outgoing email address apparently doesn't match the one that I used to sign up for the list. Is there a way to fix that?
On Aug 29, 2008, at 8:11 AM, Barb Truitt wrote:
I am trying to assign charges to a compound that contains a sulfone group. The charge assignment depends upon how I name the atoms. The atom assignment for the oxygens that are part of the sulfone group and the sulfur itself vary depending upon how they are named. How should I name them so that they are handled correctly?
The charges shouldn't depend on the names unless the element types are being deduced from the names and that deduction goes wrong, which can happen with some badly formatted PDB files. Can you provide example files where the sulfone charge assignment is going wrong?
Barb Truitt
PS - I receive the Chimera list emails, but my outgoing email address apparently doesn't match the one that I used to sign up for the list. Is there a way to fix that?
All the Chimera mailing lists are managed using Mailman software. Managing your subscription is described here: 7.3 How do I change my subscription address? --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
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