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bioRxiv · 10.1101/2023.09.01.555860

Determination of hydrogen bonds in Gromacs: new implementation to overcome the limitation

Gorelov, S.·Titov, A.·Shvetsov, A.
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Abstract

This work describes a new software algorithm associated with determination of hydrogen bonds in biomacromolecules and their environment. The already existing algorithm for determining hydrogen bond networks in Gromacs has a number of impenetrable limitations in the analysis of structures and trajectories. The new implementation of the algorithm for determining hydrogen bond networks in the form of a native Gromacs trajectory analysis module allows to quickly analyze molecular dynamics trajectories without restrictions, thereby overcoming the limitation of original algorithm. The application of the developed algorithm made it possible to obtain and analyze the networks of hydrogen bonds of the studied defensin-like protein Pentadiplandra brazzeana, as well as to study the lifetime of hydrogen bonds between the residues of this protein and water molecules. The data obtained using the new implementation coincided with the experimental one. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/555860v2_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@81727aorg.highwire.dtl.DTLVardef@82de36org.highwire.dtl.DTLVardef@1cad89forg.highwire.dtl.DTLVardef@53ec2a_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Gorelov, S., Titov, A., Shvetsov, A.. 2023-09-05. Determination of hydrogen bonds in Gromacs: new implementation to overcome the limitation. https://doi.org/10.1101/2023.09.01.555860

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