Journal
JOURNAL OF CHEMICAL INFORMATION AND MODELING
Volume 55, Issue 12, Pages 2485-2490Publisher
AMER CHEMICAL SOC
DOI: 10.1021/acs.jcim.5b00368
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Funding
- EPSRC [EP/J010588/1, EP/M022609/1]
- Royal Society University Research Fellowship
- BBSRC [BB/K016601/1]
- BrisSynBio
- BBSRC/EPSRC [BB/L01386X/1]
- BBSRC [BB/L01386X/1, BB/K016601/1] Funding Source: UKRI
- EPSRC [EP/M022609/1, EP/J010588/1] Funding Source: UKRI
- Biotechnology and Biological Sciences Research Council [BB/L01386X/1, BB/K016601/1] Funding Source: researchfish
- Engineering and Physical Sciences Research Council [EP/M022609/1, EP/J010588/1] Funding Source: researchfish
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FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions.
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