Journal Article

FZJ-2019-03386

http://join2-wiki.gsi.de/foswiki/pub/Main/Artwork/join2_logo100x88.png PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein–Lipid-Bilayer System Building

Schott-Verdugo, S. ; Gohlke, H. (Corresponding author)FZJ*

2019
American Chemical Society64160 Washington, DC

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Please use a persistent id in citations: http://hdl.handle.net/2128/22367  doi:10.1021/acs.jcim.9b00269

Abstract: We present PACKMOL-Memgen, a simple-to-use, generalized workflow for automated building of membrane-protein–lipid-bilayer systems based on open-source tools including Packmol, memembed, pdbremix, and AmberTools. Compared with web-interface-based related tools, PACKMOL-Memgen allows setup of multiple configurations of a system in a user-friendly and efficient manner within minutes. The generated systems are well-packed and thus well-suited as starting configurations in MD simulations under periodic boundary conditions, requiring only moderate equilibration times. PACKMOL-Memgen is distributed with AmberTools and runs on most computing platforms, and its output can also be used for CHARMM or adapted to other molecular-simulation packages.

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Contributing Institute(s):

1. John von Neumann - Institut für Computing (NIC)
2. Jülich Supercomputing Center (JSC)
3. Strukturbiochemie (ICS-6)

Research Program(s):

1. 511 - Computational Science and Mathematical Methods (POF3-511) (POF3-511)
2. Forschergruppe Gohlke (hkf7_20170501) (hkf7_20170501)
3. Molecular mechanisms underlying PlbF activation/deactivation via dynamic association/dissociation (hdd18_20170501) (hdd18_20170501)

Appears in the scientific report 2019

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Database coverage:
; ; Clarivate Analytics Master Journal List ; Current Contents - Physical, Chemical and Earth Sciences ; IF < 5 ; JCR ; NCBI Molecular Biology Database ; Nationallizenz ; SCOPUS ; Science Citation Index ; Science Citation Index Expanded ; Web of Science Core Collection

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