README.md
1# README PDB_AMBER2NWCHEM
2
3`pdb_amber2nwchem` is a tool to convert PDB files from the Amber
4dialect into the NWChem dialect. PDB files have standardized atom
5names for many residues of biological relevance. However, most PDB
6files do not contain Hydrogen atoms and different conventions have
7been adopted by different code communities. This tool converts
8a PDB file in the Amber convention to one following the NWChem
9conventions, so that NWChem can read it successfully.
10
11Apart from atom names the tool also converts some residue names:
12- "WAT" --> "HOH"
13- "Na+" --> "Na"
14- "K+" --> "K"
15- "Cl-" --> "Cl"
16
17to name a few examples.
18
19# References
20
21- [1] "IUPAC-IUB Commission on Biochemical Nomenclature.
22 Abbreviations and Symbols for the Description of the
23 Conformation of Polypeptide Chains. Tentative Rules (1969)".
24 Biochemistry (1970) 9, 3471-3479.
25 DOI: [10.1021/bi00820a001](https://doi.org/10.1021/bi00820a001)
26
27- [2] Charles Hoogstraten, "Correlation of hydrogen atom naming
28 systems, including diastereotopic protons." Web-page:
29 http://www.bmrb.wisc.edu/ref_info/atom_nom.tbl
30 [accessed Jan 6, 2018]
31
32- [3] IUPAC-IUBMB Joint Commission on Biochemical Nomenclature
33 and Nomenclature Commission of IUBMB, "Biochemical
34 Nomenclature and Related Documents (White Book)." 2nd Edition,
35 Portland Press, 1992, pp. 39-69. ISBN: 1-85578-005-4.
36 Part: "Amino acids, peptides and proteins", Section 3AA-1
37 "Names of Common alpha-Amino Acids".
38 DOI: [10.1351/pac198456050595](https://doi.org/10.1351/pac198456050595)
39