Comparison of charge derivation methods applied to amino acid parameterization
When using non-natural amino acids in computational simulations of proteins, it is necessary to ensure appropriate parameterization of the new amino acids toward the creation of appropriate input files. In particular, the charges on the atoms may have to be derived de novo and ad hoc for the new spe...
Saved in:
| Main Authors: | , , |
|---|---|
| Other Authors: | |
| Format: | Article |
| Language: | English |
| Published: |
2019
|
| Subjects: | |
| Online Access: | https://hdl.handle.net/10356/106848 http://hdl.handle.net/10220/49658 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| Institution: | Nanyang Technological University |
| Language: | English |
| Summary: | When using non-natural amino acids in computational simulations of proteins, it is necessary to ensure appropriate parameterization of the new amino acids toward the creation of appropriate input files. In particular, the charges on the atoms may have to be derived de novo and ad hoc for the new species. As there are many variables in the charge derivation process, an investigation was devised to compare different approaches and determine their effect on simulations. This was done with the purpose to identify the methods which produced results compatible with the existing parameters. It was found in this study that all analyzed charge derivation methods reproduce with sufficient accuracy the literature values and can be used with confidence when parameterizing novel species. |
|---|