[Chimera-users] energy minimization

[Eric Pettersen]

Hi Sara,
	There are a couple of problems here.  One is that the heme coordinates / bond lengths aren’t very good, so Chimera’s estimates for the atom types is wrong for some of the atoms.  The other problem is that because the iron is displaced out of the porphyrin ring, addh is adding hydrogens to the inside of the ring that would normally be prevented by the presence of the iron.  Those hydrogens repel the iron of course.
	So, to correct things, you need to:

1) Delete all hydrogens
2) Correct the atom types
3) Add the hydrogens back
4) Delete inward-facing porphyrin-ring hydrogens
5) Add charges
6) Minimize

The commands (Favorites→Command Line) corresponding to those steps are:

1) “del H”
2) “defattr /path/to/heme.defattr raise false”  (I have attached the heme.defattr file) 
3) “addh”
4) “del :hem at hd”
5) “addch”  (this will take awhile with AM1-BCC charges)
6) Minimize however you were doing it before.

I have also attached a session with all the above steps performed.  The iron is not yet planar with the ring, but additional minimization will undoubtedly get it there.

—Eric

	Eric Pettersen
	UCSF Computer Graphics Lab




> On Jul 15, 2019, at 6:23 AM, sara20 at mail.ustc.edu.cn wrote:
> 
> Dear 
> I am trying to minimize a structure with HEME cofactor. I added heme frcmod and prep files from Amber parameter database in parm and prep folders respectively.I minimized the structure at different steps of steepest descent from 100 to 1000.But in all the structures FE of heme is not well aligned with HEME structure (it is pointed out of structure).I tried with both all atom and united atom frcmod and prep files but the results are same.Please find attached the minimized structure. Kindly tell me where am I wrong. Any help would be appreciated. Thank you
> 
> Regards
> Sara
> <min1Refined_model7.pdb>_______________________________________________
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