Abstract
Recently, the ABEEM/MM method (atom-bond electronegativity equalization method fused into molecular mechanics) has successfully been applied to study polypeptide conformations. In order to further test the reliability of this method as well as the transferability of the parameters (including ABEEM and force field parameters), molecular dynamics simulation studies on Crambin and BPTI (298 K, in vacuo) have been performed in terms of ABEEM/MM fluctuating charge force field. Some of their structural properties were obtained, and relative to the X-ray structures, the root-mean-square deviations (RMSD) of bond lengths, bond angles and key dihedral angles, and the coordinate RMSDs of atoms were calculated. The ABEEM/MM results are fairly consistent with those from X-ray experiment.
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