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Hello,</div>
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with Avogadro I built and optimized simple tri-peptide which I read as pdb into ChimeraX, see the attachments.</div>
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When I wanted to display coulombic potential, I got the following error message below.</div>
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Looks like Avogadro's pdb protocol does not fit for ChimeraX...although all atoms and bonds in the tripeptide example are correct. </div>
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Any help, please ? </div>
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The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics:
<div>/A GLU 2 CG</div>
<div>/A GLU 2 OE2</div>
<div>/A GLU 2 CA</div>
<div>/A GLU 2 CD</div>
<div>/A GLU 2 CB</div>
<div>/A GLU 2 OE1</div>
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<div>Using Amber 20 recommended default charges and atom types for standard residues</div>
Hydrogen /A LEU 3 HO bonded to atom that should not have hydrogens (/A LEU 3 OXT)<br>
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<div class="PlainText">-- <br>
doc. RNDr. Miroslav Iliaš, PhD.<br>
<br>
Katedra chémie<br>
Fakulta prírodných vied<br>
Univerzita Mateja Bela<br>
Tajovského 40<br>
97401 Banská Bystrica<br>
tel: +421 48 446 7351<br>
email : Miroslav.Ilias@umb.sk<br>
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<span style="font-size:13.3333px">Miroslav Iliaš, PhD.</span><br>
Department of Chemistry<br>
Faculty of Natural Sciences<br>
Matej Bel University<br>
Tajovského 40<br>
97401 Banska Bystrica<br>
Slovakia<br>
tel: +421 48 446 7351<br>
email : Miroslav.Ilias@umb.sk</div>
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