title: PyCPR - a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures.
abstract: Conjugate peak refinement (CPR) is a powerful and robust method to search transition states on a molecular potential energy surface. Nevertheless, the method was to the best of our knowledge so far only implemented in CHARMM. In this paper, we present PyCPR, a new Python-based implementation of the CPR algorithm within the pDynamo framework. We provide a detailed description of the theory underlying our implementation and discuss the different parts of the implementation. The method is applied to two different problems. First, we illustrate the method by analyzing the gauche to anti-periplanar transition of butane using a semiempirical QM method. Second, we reanalyze the mechanism of a glycyl-radical enzyme, namely of 4-hydroxyphenylacetate decarboxylase (HPD) using QM/MM calculations. In the end, we suggest a strategy how to use our implementation of the CPR algorithm. The integration of PyCPR into the framework pDynamo allows the combination of CPR with the large variety of methods implemented in pDynamo. PyCPR can be used in combination with quantum mechanical and molecular mechanical methods (and hybrid methods) implemented directly in pDynamo, but also in combination with external programs such as ORCA using pDynamo as interface. PyCPR is distributed as free, open source software and can be downloaded from http://www.bisb.uni-bayreuth.de/index.php?page=downloads . Graphical Abstract PyCPR is a search tool for finding saddle points on the potential energy landscape of a molecular system.
authors.affiliation: Computational Biochemistry, University of Bayreuth, Universitätsstr. 30, NW I, 95447, Bayreuth, Germany.
authors.forename: Florian J
authors.initials: FJ
authors.lastname: Gisdon
authors.affiliation: Computational Biochemistry, University of Bayreuth, Universitätsstr. 30, NW I, 95447, Bayreuth, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Culka
authors.affiliation: Computational Biochemistry, University of Bayreuth, Universitätsstr. 30, NW I, 95447, Bayreuth, Germany. ullmann@uni-bayreuth.de.
authors.forename: G Matthias
authors.identifier: http://orcid.org/0000-0002-6350-798X
authors.initials: GM
authors.lastname: Ullmann
keywords: Minimum energy path; Potential energy surface; Reaction mechanism; Saddle point; Transition state search; pDynamo