Paper Citing NAMD - Abstract
Casanovas, Jordi; Zanuy, David; Nussinov, Ruth; Aleman, Carlos
Identification of the intrinsic conformational properties of 1-aminocyclobutane-1-carboxylic acid
CHEMICAL PHYSICS LETTERS, 429:558-562, OCT 5 2006
We have used quantum mechanical calculations at the B3LYP/6-31+G(d,p) and MP2/6-31+G(d,p) levels to determine the conformational preferences of the N-acetyl-N-methylamide derivative of I-aminocyclobutane-l-carboxylic acid in the gas-phase and water solution. Results indicate that the backbone flexibility of this amino acid is restricted by the cyclic nature of the side chain, the relative stability of the different minimum energy conformations being almost independent of the environment. Furthermore, a set of force-field parameters for classical molecular dynamics simulations was developed for the investigated amino acid. Simulations in different environments were performed to demonstrate the reliability of such parameters. (c) 2006 Elsevier B.V. All rights reserved.
