[Chimera-users] Fe in chimera antechamber

Elaine Meng meng at cgl.ucsf.edu
Tue Nov 6 10:16:44 PST 2007

Hi "S"
We are glad you like Chimera.

(1) HEM and FE charges.  AMBER charges are assigned for the protein,  
but not for the nonstandard residue HEM/FE.  Since FE is only one  
atom, it will put whatever integer charge you specify on that atom  
(without trying to "calculate" the charge).  You can see the assigned  
charge by labeling the atom with its charge value (see below) or  
looking in the charge column of the output Mol2 file, if you wrote it  
out.  The Add Charge dialog will always show +2 for your FE because  
it always uses the same method to guess what the charge should be,  
but that does not mean the currently assigned charge is +2.  I just  
tested this by specifying FE charge +7 and then labeling the atom;  
Add Charge did assign +7.  For the example structure PDB 1a6m,  
however, +2 is the correct charge for FE and -4 the correct charge  
for the rest of HEM, protoporphyrin IX.

To label atoms with their charges, select the atoms of interest, then  
either use the commands:

labelopt info charge
label sel

or use the menu Actions... Label... other... and choose the attribute  
"charge" from the pulldown menu in the labeling dialog.

(2) Charge set.  Only all-atom charges can be assigned by Chimera,  
not united-atom (where the nonpolar CH CH2 and CH3 are treated as  
single points).

I hope this helps,
Elaine C. Meng, Ph.D.                          meng at cgl.ucsf.edu
UCSF Computer Graphics Lab and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Nov 6, 2007, at 7:58 AM, snoze pa wrote:

> Hi, I am new in this mailing list but found chimera more useful  
> than any other software. I was building a protein that contain  
> HEME. When I was calculating the charge using chimera interface,  
> then it is asking for HEM[FE] and HEM[nonFE] formal charge. I know  
> chimera is using MMTK and AMBER forcefield. If I will give the  
> default value then it is assigning +2 charge to Fe, which is not a  
> match based on AMBER forcefield.  Meanwhile I try to change the  
> Formal charge manually, but still it gives the same +2 for Fe.  
> Anybody used chimera to prepare a protein having heme for dock or  
> geometry build.
>  My another question is: Is it possible in chimera to merge  
> nonpolar hydrogen charges on the heavy atoms, the technique used in  
> autodock.
> I will highly appreciate your help and suggestions in this matter.
> thanks in advance.
> s

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