[Chimera-users] applying charges calculated by DFT to ligands in protein models

Anne-Frances Miller afm at uky.edu
Mon Sep 21 13:35:40 PDT 2015

Dear Sir or Madam,
Our protein has a bound FMN and the various tools accessible via Chimera are not able to apply charges to the atoms in FMN.  However I have NBO charges for all the atoms from DFT calculations. Is there a way I can provide these to the FMN in my pdb file or in my Chimera session in order to then display a Coulomb electrostatic potential for the protein + FMN?  My charges are not simply +1 or -1, but fractional charges for each atom.  Can Chimera accommodate this ?  If not, no problem, I will still benefit greatly even if all I can do is add -1 to the one atom at which most of the excess electron density is concentrated.

Many Thanks,

Anne-Frances Miller
Professor of Chemistry
Director, Magnetic Resonance Centre
University of Kentucky
Dept. Chemistry, 505 Rose Street
Lexington KY 40506-0055

“You never change things by fighting the existing reality. To change something, build a new model that makes the existing model obsolete.” Buckminster Fuller 

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