[Chimera-users] energy minimization

sara20 at mail.ustc.edu.cn sara20 at mail.ustc.edu.cn
Mon Jul 15 20:44:30 PDT 2019

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.

-----Original Messages-----
From:"Eric Pettersen" <pett at cgl.ucsf.edu>
Sent Time:2019-07-16 06:55:59 (Tuesday)
To: sara20 at mail.ustc.edu.cn
Cc: "chimera-users at cgl.ucsf.edu BB" <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 Pettersen
UCSF Computer Graphics Lab

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