[Chimera-users] Minimization and mystery nonstandard HIS atom name

Eric Pettersen pett at cgl.ucsf.edu
Thu Aug 22 16:06:43 PDT 2013


Hi Jason,
	I think this is a problem that was fixed in May of last year, i.e. in versions 1.6.2 and later.  What version are you using?    If you are using 1.6.2+, please send me your structure file so I can track down the problem.

--Eric

On Aug 22, 2013, at 2:35 PM, Jason L Burkhead <jlburkhead at uaa.alaska.edu> wrote:

> I am trying to minimize a protein structure and run into the following error:
> 
> 'No MMTK name for atom "HND1" in standard residue "HIS"'
> 
> My .pdb file specifies this atom as ND1, and if I change it to HND1 it still gives me the same error. Does anyone have any suggestions for a solution?
> 
> The reply log is below:
> 
> Thanks
> Jason
> 
> No incomplete side chains
> No SEQRES records for COMMD1_C_terminus_c.2.0.pdb (#0) chain A; guessing terminii instead
> Chain-initial residues that are actual N terminii: GLY 1.A
> Chain-initial residues that are not actual N terminii: 
> Chain-final residues that are actual C terminii: ASN 73.A
> Chain-final residues that are not actual C terminii: 
> 42 hydrogen bonds
> Hydrogens added
> Charge model: AMBER ff99SB
> Non-standard atom names:
> HIS HND1 (HIS 17.A HND1, HIS 22.A HND1)
> Total charge for #0: -4.000
> Correct charges are unknown for 1 non-standard atom names in otherwise standard residues
> 
> Charges of 0.0 were assigned to the unknown atoms
> 
> Details in reply log
> 
> No MMTK name for atom "HND1" in standard residue "HIS"
> 
> 
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