applying charges calculated by DFT to ligands in protein models
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 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
Dear Anne-Frances, Yes, you can assign your own atomic partial charges. If you’re doing it for the purposes of energy minimization, it is still necessary to run Add Charge because that tool assigns the atom types needed for minimization. In Add Charge, just choose the quick Gasteiger method since you will be over-writing the charges with your own values anyway. The (somewhat circuitous) process is outlined here: <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#user-specified> As mentioned in that link, to assign your custom charges you would then need to either use a series of “setattr” commands, each assigning the charge to a single atom in the FMN residue, or create an attribute assignment file listing all of the charges for the atoms of that residue and read it in with “defattr” (or equivalently, the Define Attribute tool). See that link for details. If you aren’t doing energy minimization, for example if you’re just going to color the surface by electrostatic potential, you wouldn’t have to run Add Charge. You’d just need to assign your charges with setattr or defattr as above, or read them in along with the coordinates of the FMN molecule if you had it in a separate Mol2 or PQR file, as described in the bottom section of this page. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html> I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2015, at 1:35 PM, Anne-Frances Miller <afm@uky.edu> wrote:
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
This is very helpful, Thank you Elaine. 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
On Sep 21, 2015, at 7:25 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Dear Anne-Frances, Yes, you can assign your own atomic partial charges. If you’re doing it for the purposes of energy minimization, it is still necessary to run Add Charge because that tool assigns the atom types needed for minimization. In Add Charge, just choose the quick Gasteiger method since you will be over-writing the charges with your own values anyway. The (somewhat circuitous) process is outlined here:
<http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/minimize/minimize.html#user-specified>
As mentioned in that link, to assign your custom charges you would then need to either use a series of “setattr” commands, each assigning the charge to a single atom in the FMN residue, or create an attribute assignment file listing all of the charges for the atoms of that residue and read it in with “defattr” (or equivalently, the Define Attribute tool). See that link for details.
If you aren’t doing energy minimization, for example if you’re just going to color the surface by electrostatic potential, you wouldn’t have to run Add Charge. You’d just need to assign your charges with setattr or defattr as above, or read them in along with the coordinates of the FMN molecule if you had it in a separate Mol2 or PQR file, as described in the bottom section of this page. <http://www.rbvi.ucsf.edu/chimera/docs/ContributedSoftware/addcharge/addcharge.html>
I hope this helps, Elaine ---------- Elaine C. Meng, Ph.D. UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 21, 2015, at 1:35 PM, Anne-Frances Miller <afm@uky.edu> wrote:
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
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Anne-Frances Miller -
Elaine Meng