Journal
JOURNAL OF CHEMICAL INFORMATION AND MODELING
Volume 59, Issue 6, Pages 2522-2528Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jcim.9b00269
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Funding
- Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) [267205415, SFB 1208]
- [FOR 2518]
- [GO 1367/2-1]
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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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