<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Jason,<div><span class="Apple-tab-span" style="white-space:pre"> </span>I think this is a problem that was fixed in May of last year, <i>i.e.</i> 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.</div><div><br></div><div>--Eric</div><div><br><div><div>On Aug 22, 2013, at 2:35 PM, Jason L Burkhead <<a href="mailto:jlburkhead@uaa.alaska.edu">jlburkhead@uaa.alaska.edu</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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<div>I am trying to minimize a protein structure and run into the following error:</div>
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<div>'No MMTK name for atom "HND1" in standard residue "HIS"'</div>
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<div>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?</div>
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<div>The reply log is below:</div>
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<div>Thanks</div>
<div>Jason</div>
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<div>No incomplete side chains</div>
<div>No SEQRES records for COMMD1_C_terminus_c.2.0.pdb (#0) chain A; guessing terminii instead</div>
<div>Chain-initial residues that are actual N terminii: GLY 1.A</div>
<div>Chain-initial residues that are not actual N terminii: </div>
<div>Chain-final residues that are actual C terminii: ASN 73.A</div>
<div>Chain-final residues that are not actual C terminii: </div>
<div>42 hydrogen bonds</div>
<div>Hydrogens added</div>
<div>Charge model: AMBER ff99SB</div>
<div>Non-standard atom names:</div>
<div><span class="Apple-tab-span" style="white-space:pre"></span>HIS HND1 (HIS 17.A HND1, HIS 22.A HND1)</div>
<div>Total charge for #0: -4.000</div>
<div>Correct charges are unknown for 1 non-standard atom names in otherwise standard residues</div>
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<div>Charges of 0.0 were assigned to the unknown atoms</div>
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<div>Details in reply log</div>
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<div>No MMTK name for atom "HND1" in standard residue "HIS"</div>
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