ArticleJournal of computational chemistry2021
CAN: A new program to streamline preparation of molecular coordinate files for molecular dynamics simulations.
Article in Journal of computational chemistry, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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2 citing papers in PubMed.
- Structural Analysis of Non-native Peptide-Based Catalysts Using 2D NMR-Guided MD Simulations.The journal of physical chemistry. A · 2023Article
- Optimizing the Local Chemical Environment on a Bifunctional Helical Peptide Scaffold Enables Enhanced Enantioselectivity and Cooperative Catalysis.Organic letters · 2022Article
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3 authors.
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Abstract
Preparing molecular coordinate files for molecular dynamics (MD) simulations can be a very time-consuming process. Herein we present the development of a user-friendly program that drastically reduces the time required to prepare these molecular coordinate files for MD software packages such as AmberTools. Our program, known as charge atomtype naming (CAN), creates and uses a library of structures such as amino acid monomers to update the charge, atom type, and name of atoms in any molecular structure (mol2) file. We demonstrate the utility of this new program by rapidly preparing structural files for MD simulations for polypeptides ranging from small molecules to large protein structures. Both native and non-native amino acid residues are easily handled by this new program.
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