[Chimera-users] Fe in chimera antechamber

[Elaine Meng]

On Nov 6, 2007, at 11:32 AM, snoze pa wrote:
>
>  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.
>
> 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?

Don't worry about this message - GAFF type is only needed for energy- 
minimization in Chimera, and is not used or needed by DOCK.
>
> 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 don't know what you mean by "precalculated charges for amber" - is  
there some file or online information for HEM charges you are looking  
at?  If so, whoever made it probably used 6-31G* and RESP to get  
those charges, rather than Antechamber and AM1-BCC.  For nonstandard  
residues like the HEM, you can actually use whatever charges you  
want, but it is a little more complicated than just using  
Antechamber.  To get different charges in the Mol2 which you will  
later use in DOCK, you could

either
(1) just edit the output Mol2 file and change the charges
or
(2) run Dock Prep without writing Mol2, reassign charges, then use  
File... Save Mol2.  For more information on reassigning charges, see
http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/minimize/ 
minimize.html#user-specified

#1 might be easier in your situation, at least if your HEM atom names  
match the ones in the AMBER data you are looking at.
Best
Elaine