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@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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