[Chimera-users] Hydrogen issue with minimization

[Elaine Meng]

Hi Guillaume,
If you look at GLU 23 in chain A, you can see that it is truncated to only a CB atom (as if it were an ALA instead), so that when it gets hydrogens, it gets 3 hydrogens since the side chain is only a methyl group, and these hydrogen names are not expected for a GLU residue.  So maybe you want to run Dock Prep with the option to repair truncated sidechains turned on before adding hydrogens, charges, etc. and then minimizing.

When you get an error about a specific residue you should look carefully at the atoms of that residue.
I hope this helps,
Elaine
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Elaine C. Meng, Ph.D.                       
UCSF Chimera(X) team
Department of Pharmaceutical Chemistry
University of California, San Francisco

> On Feb 8, 2023, at 4:30 AM, Guillaume Grataloup via Chimera-users <chimera-users at cgl.ucsf.edu> wrote:
> 
> Dear support,
> 
> I currently trying to perform a minimization on a hERG canal pdb file but I run into an issue I didn't manage to solve:
> "Residue #0:23.A (GLU/glutamic_acid) should have either atom HB1 or HB3, but not both"
> Maybe the problem comes from the pdb file, I put it in attachment just in case it can help understand the issue.
> Also my Chimera version is 1.16 and I'm on Windows
> 
> Thank you in advance
> 
> Guillaume Grataloup
> 5th year bioengineering studient at Polytech Nice Sophia, France
> <hERGts_compiled.pdb>