ABSTRACT

Aim –Earlier researches were unable to unfold an easy use of the existing energy minimisation algorithm that can be used to remove the stoichiometric clashes before MD simulation. The research aims to identify the effective and feasible energy minimisation algorithm that can be applied before MD simulation to conduct energy minimisation. Methods- the protein with id 1A5Q is chosen from the RCSB-PDB database and the CHARMMM files are obtained. Based on them the energy minimisation of the protein is conducted in three different algorithms with respect to three different conditions (implicit, explicit and vacuum). Results-SD is the fastest among three but ABNR reaches more -?G whereas conjugate gradient minimises more but takes ample time. Conclusion- A cocktail of SD and ABNR needs to be applied in case of energy minimisation. Keywords: CHARMM, ABNR, SD, Conjugate gradient, MD simulation, GBSW, GBMV, energy minimisation, protein ensemble, protein energy, electrostatic interactions, covalent bonds
Publication date: 01/12/2021

https://ijbpas.com/pdf/2021/December/MS_IJBPAS_2021_DEC_SPCL_2052.pdf

Download PDF
https://doi.org/10.31032/IJBPAS/2021/10.12.2052