This title appears in the Scientific Report :
2019
Please use the identifier:
http://dx.doi.org/10.1021/acs.jcim.9b00269 in citations.
Please use the identifier: http://hdl.handle.net/2128/22367 in citations.
PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein–Lipid-Bilayer System Building
PACKMOL-Memgen: A Simple-To-Use, Generalized Workflow for Membrane-Protein–Lipid-Bilayer System Building
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...
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Personal Name(s): | Schott-Verdugo, Stephan |
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Gohlke, Holger (Corresponding author) | |
Contributing Institute: |
Strukturbiochemie; ICS-6 Jülich Supercomputing Center; JSC John von Neumann - Institut für Computing; NIC |
Published in: | Journal of chemical information and modeling, 59 (2019) 6, S. 2522-2528 |
Imprint: |
Washington, DC
American Chemical Society64160
2019
|
DOI: |
10.1021/acs.jcim.9b00269 |
PubMed ID: |
31120747 |
Document Type: |
Journal Article |
Research Program: |
Molecular mechanisms underlying PlbF activation/deactivation via dynamic association/dissociation Forschergruppe Gohlke Computational Science and Mathematical Methods |
Link: |
Restricted Published on 2019-05-23. Available in OpenAccess from 2020-05-23. Published on 2019-05-23. Available in OpenAccess from 2020-05-23. Restricted |
Publikationsportal JuSER |
Please use the identifier: http://hdl.handle.net/2128/22367 in citations.
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. |