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bioRxiv · 10.1101/2023.09.05.556379

Backmapping with Mapping and Isomeric Information

Kim, S.
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Abstract

I present a powerful and flexible backmapping tool named Multiscale Simulation Tool (mstool) that converts a coarse-grained (CG) system into all-atom (AA) resolution and only requires AA to CG mapping and isomeric information (cis/trans/dihedral/chiral). The backmapping procedure includes two simple steps: a) AA atoms are randomly placed near the corresponding CG beads according to the provided mapping scheme. b) Energy minimization is performed with two modifications in the AA force field (FF). First, nonbonded interactions are replaced with cosine functions to ensure numerical stability. Second, additional torsions are imposed to maintain molecules isomeric properties. To test the simplicity and robustness of the tool, I backmapped multiple membrane and protein CG structures into AA resolution, including a four-bead CG lipid model (resolution increased by a factor of 34) without using intermediate resolution. The tool is freely available at github.com/ksy141/mstool. TABLE OF CONTENTS (TOC) O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=109 SRC="FIGDIR/small/556379v2_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@5704aforg.highwire.dtl.DTLVardef@f4bdf6org.highwire.dtl.DTLVardef@1e362feorg.highwire.dtl.DTLVardef@1781ade_HPS_FORMAT_FIGEXP M_FIG C_FIG

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Kim, S.. 2023-09-06. Backmapping with Mapping and Isomeric Information. https://doi.org/10.1101/2023.09.05.556379

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