[Chimera-users] energy minimization

Eric Pettersen pett at cgl.ucsf.edu
Tue Jul 16 11:33:22 PDT 2019

It turns out that without a cofactor stabilizing the position of the iron, the ff14SB force field parameters are such that the iron will minimize to be somewhat non-planar with the porphyrin ring.  For instance if I take the 2j0p structure and delete everything but the heme and then run 1000 steps of steepest descent, the iron moves out of the plane of the ring.

The OPLS force field has explicit parameters for maintaining the ring planarity of the iron, but that is beyond the scope of Chimera.  You would have to run Amber of some other package yourself.


> On Jul 15, 2019, at 8:44 PM, sara20 at mail.ustc.edu.cn wrote:
> Hi Eric
> Thanks for your suggestions. I tried the mentioned steps but still facing the same issue (see attached file). I forgot to mention that I am minimizing the modelled structure, maybe that's why it's creating this problem. In modelling I modelled the structure with heme and also with out heme (and later on pasted the heme coordinates from template to model structure). I minimized both structures and ended up with the same problem. I am not sure where am I making mistake. I'd be grateful if you could guide me more.
> Regards
> Sara
> -----Original Messages-----
> From:"Eric Pettersen" <pett at cgl.ucsf.edu <mailto:pett at cgl.ucsf.edu>>
> Sent Time:2019-07-16 06:55:59 (Tuesday)
> To: sara20 at mail.ustc.edu.cn <mailto:sara20 at mail.ustc.edu.cn>
> Cc: "chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu> BB" <chimera-users at cgl.ucsf.edu <mailto:chimera-users at cgl.ucsf.edu>>
> Subject: Re: [Chimera-users] energy minimization
> 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
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