[chimerax-users] following heavy (non-hydrogen) atoms are missing

[Ilias Miroslav, doc. RNDr., PhD.]

Hello,

with Avogadro I built and optimized simple tri-peptide which I read as pdb into ChimeraX, see the attachments.

When I wanted to display coulombic potential, I got the following error message below.

Looks like Avogadro's  pdb protocol does not fit for ChimeraX...although all atoms and bonds in the tripeptide example are correct.

Any help, please ?

The following heavy (non-hydrogen) atoms are missing, which may result in inaccurate electrostatics:
/A GLU 2 CG
/A GLU 2 OE2
/A GLU 2 CA
/A GLU 2 CD
/A GLU 2 CB
/A GLU 2 OE1

Using Amber 20 recommended default charges and atom types for standard residues
Hydrogen /A LEU 3 HO bonded to atom that should not have hydrogens (/A LEU 3 OXT)

--
doc. RNDr. Miroslav Iliaš, PhD.

Katedra chémie
Fakulta prírodných vied
Univerzita Mateja Bela
Tajovského 40
97401 Banská Bystrica
tel: +421 48 446 7351
email : Miroslav.Ilias at umb.sk

Miroslav Iliaš, PhD.
Department of Chemistry
Faculty of Natural Sciences
Matej Bel University
Tajovského 40
97401 Banska Bystrica
Slovakia
tel: +421 48 446 7351
email :  Miroslav.Ilias at umb.sk

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