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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