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

Jason L Burkhead jlburkhead at uaa.alaska.edu
Thu Aug 22 14:35:24 PDT 2013

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:


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:
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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