Abstract. Maximum entropy procedures for estimating coarse-grain parameters from molecular dynamics (MD) simulation data are considered within the specific context of the sequence-dependent cgDNA rigid-base model of DNA. We describe a quite general approach that exploits a maximum absolute entropy principle to fit an observed matrix of covariances subject to the constraint of only allowing a prescribed sparsity pattern of nearest-neighbor interactions in the free energy. We also allow indefinite local stiffness-matrix parameter blocks that nevertheless always generate a positive-definite model stiffness matrix. Beginning from a database of atomic-resolution MD simulations of a library of short DNA oligomers in explicit solvent, these procedures deliver a complete parameter set for the cgDNA model. Due to the intrinsic linear structure of DNA and the convergence characteristics of the MD time series data, the maximum absolute entropy parameter set yields significantly improved predictions of persistence lengths, when compared to a previous parameter set that was fit to the same MD data, but using a maximum relative entropy fitting principle and local stiffness-matrix parameter blocks that were constrained to be semidefinite.Key words. entropy principles, parameter estimation, molecular modeling, statistical mechanics AMS subject classifications. 62H12, 82B05, 82D60, 15A83, 15A09 DOI. 10.1137/16M10860911. Introduction. An important problem in molecular biology is to understand how the mechanical properties of DNA depend on the sequence of bases along its two backbones. Properties that influence bending, twisting, shearing, and stretching in different directions along and across the two strands are believed to be essential in various biological processes such as DNA looping [34], nucleosome positioning [35], and other DNA-protein interactions, and gene regulation [26], all of which depend on the probability of DNA to adopt various three-dimensional configurations [4]. Consequently models at differing length scales are needed to quantify how the mechanical properties of DNA depend upon its sequence. The intermediate scales of a few tens to a few hundreds of base pairs are of particular biological interest. The study of sequence-dependent effects at such scales requires the development of specialized coarse-grain models, because, with contemporary computational resources, all-atom molecular dynamics (MD) simulations at these lengths remain intensive, particularly given the large number of possible sequences, while sequence-dependent behavior is