I built short peptides in Avagadro, using Build--->insert--->peptide. After constructing the short peptides of 4 amino acids(tetrapeptide). Under the drop-down, View--->Atomic properties, I am able to read the partial charges on each atom. Where do I find the reference for those partial charges? Is it taken from AMBER / CHARMM? How do I find that out?
Dear Vigneshwaran Kannan ,
Not sure if this is what you are looking for, but I found the following info related to your question:
https://discuss.avogadro.cc/t/partial-charges/248
The calculation of the Gasteiger Marsili (PEOE) partial charges is based on:
Gasteiger, J., & Marsili, M. (1980). Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges. Tetrahedron, 36(22), 3219-3228.
Best regards.
Dear Rob Keller ,
I am looking for the reference for the partial charges shown by Avagadro. Thanks in advance
Hi Vigneshwaran! Abogadro has a number built-in force fields. So when you build your molecule you shall look up in Extensions-> Molecular Mechanics-> Set up force field. I think the default is MMFF94 (unless you changed the default).
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