[Chimera-users] Fe in chimera antechamber

snoze pa snoze.pa at gmail.com
Tue Nov 6 11:32:48 PST 2007

Dear Elaine,

 Thank you very much for your detailed reply. I worked on the PDB id 1A6M as
suggested by you and followed the same instructions. I used +2 for FE and -4
for HEME and found following message at the end. The details about the
calculations are also attached in this mail along with mol2 file. Before
calculation, I removed the water, oxy and so4 in het entry and did the
calculations with protein and heme alone.

Here is what I am getting at the end using BC-AM1

Charges for residue HEM[non-FE] determined
Total charge for #0: 2.0001
Unable to find GAFF type for #0:154.het at FE

what is this message?

log file along with the charge snapshot is attached with this mail.

So, Can I use this mol2 file in DOCK 6 calculations? I am lil worried since
the pre-calculated charges for amber are different from the the one I am
getting using chimera and antechamber combination.

I will highly appreciate your reply and suggestions.

Thanks in advance,

On Nov 6, 2007 12:16 PM, Elaine Meng <meng at cgl.ucsf.edu> wrote:

> 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
> -----
> 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
>                      http://www.cgl.ucsf.edu/home/meng/index.html
> 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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