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arXiv · 1206.3909

Amino-acid-dependent main-chain torsion-energy terms for protein systems

Yoshitake Sakae·Yuko Okamoto
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Abstract

Many commonly used force fields for protein systems such as AMBER, CHARMM, GROMACS, OPLS, and ECEPP have amino-acid-independent force-field parameters of main-chain torsion-energy terms. Here, we propose a new type of amino-acid-dependent torsion-energy terms in the force fields. As an example, we applied this approach to AMBER ff03 force field and determined new amino-acid-dependent parameters for $\psi$ and $\psi'$ angles for each amino acid by using our optimization method, which is one of the knowledge-based approach. In order to test the validity of the new force-field parameters, we then performed folding simulations of $\alpha$-helical and $\beta$-hairpin peptides, using the optimized force field. The results showed that the new force-field parameters gave structures more consistent with the experimental implications than the original AMBER ff03 force field.

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BibTeXRIS

Yoshitake Sakae, Yuko Okamoto. 2012-06-18. Amino-acid-dependent main-chain torsion-energy terms for protein systems. https://doi.org/10.1063/1.4774159

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