Hi, I have used the peptide builder of Avogadro for scientific research. I have used the geometries obtained with peptide builder as starting point for geometry optimization with QM code. I would like to know if there is any reference to cite from which Avogadro takes the amino acids structures used to build peptides.
Thanks in advance!
Giulia
I’m not sure you need to go into that level of detail, but the individual amino acids in the peptide builder were optimized using the PM6 method:
Stewart, J.J.P. Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements. J Mol Model 13, 1173–1213 (2007). Optimization of parameters for semiempirical methods V: Modification of NDDO approximations and application to 70 elements | Journal of Molecular Modeling
To be specific, I generated tetramers of a particular amino acid, optimized the geometry and took the “central” residues for the individual amino acid geometries.
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