CAMDAS - AN AUTOMATED CONFORMATIONAL-ANALYSIS SYSTEM USING MOLECULAR-DYNAMICS

We present an automated conformational analysis program, CAMDAS (Confo rmational Analyzer with Molecular Dynamics And Sampling). CAMDAS perfo rms molecular dynamics (MD) calculations for a target molecule and sam ples conformers from the trajectory of the MD. The program then evalua tes the similarities between each of the sampled conformers in terms o f the root-mean-square deviations of the atomic positions, clusters si milar conformers, and finally prints out the clustered conformers. Thi s MD-based conformational analysis is a broadly used method, and CAMDA S is intended to provide a convenient framework for the method. CAMDAS has the ability to find the representative conformers automatically f rom an arbitrarily given structure of the molecule. The accuracy of th e program was examined using N-acetylalanine-N'-methylamide, and the o btained result was consistent with that of the systematic search metho d. In the test calculation of cyclodecane, CAMDAS could identify most of the known conformers and their conformational enantiomers by examin ing only 5000 conformers. In addition, the potential-scaled method, wh ich we have developed previously as an accelerating technique for MD, could find two additional conformers of cyclodecane that have not been reported. CAMDAS presents a convenient way to find the energetically possible conformers of a molecule, which is needed especially in the e arly stage of drug design.