PyCPR – a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures

Title data

Gisdon, Florian J. ; Culka, Martin ; Ullmann, G. Matthias:
PyCPR – a python-based implementation of the Conjugate Peak Refinement (CPR) algorithm for finding transition state structures.
In: Journal of Molecular Modeling. Vol. 22 (2016) . - 242.
ISSN 0948-5023
DOI: https://doi.org/10.1007/s00894-016-3116-8

Official URL:

Abstract in another language

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.

Further data

Item Type:	Article in a journal
Refereed:	Yes
Keywords:	Potential energy surface; Saddle point; Transition state search; Minimum energy path; Reaction mechanism; pDynamo
Institutions of the University:	Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Professor Bioinformatics/Structural Biology > Professor Bioinformatics/Structural Biology - Univ.-Prof. Dr. Matthias Ullmann Faculties Faculties > Faculty of Biology, Chemistry and Earth Sciences Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry Faculties > Faculty of Biology, Chemistry and Earth Sciences > Department of Chemistry > Professor Bioinformatics/Structural Biology
Result of work at the UBT:	Yes
DDC Subjects:	500 Science > 540 Chemistry
Date Deposited:	30 Jun 2022 08:03
Last Modified:	26 Jan 2024 11:30
URI:	https://eref.uni-bayreuth.de/id/eprint/70230