Minimization and mystery nonstandard HIS atom name

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"

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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participants (2)
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Eric Pettersen
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Jason L Burkhead