MMPBSA.py: An Efficient Program for End-State Free Energy Calculations
Bill R Miller
1
,
T Dwight Mcgee
1
,
Jason M. Swails
1
,
Nadine Homeyer
2
,
H Gohlke
2
,
Adrian Roitberg
1
Publication type: Journal Article
Publication date: 2012-08-16
scimago Q1
wos Q1
SJR: 1.482
CiteScore: 9.8
Impact factor: 5.5
ISSN: 15499618, 15499626
PubMed ID:
26605738
Physical and Theoretical Chemistry
Computer Science Applications
Abstract
MM-PBSA is a post-processing end-state method to calculate free energies of molecules in solution. MMPBSA.py is a program written in Python for streamlining end-state free energy calculations using ensembles derived from molecular dynamics (MD) or Monte Carlo (MC) simulations. Several implicit solvation models are available with MMPBSA.py, including the Poisson-Boltzmann Model, the Generalized Born Model, and the Reference Interaction Site Model. Vibrational frequencies may be calculated using normal mode or quasi-harmonic analysis to approximate the solute entropy. Specific interactions can also be dissected using free energy decomposition or alanine scanning. A parallel implementation significantly speeds up the calculation by dividing frames evenly across available processors. MMPBSA.py is an efficient, user-friendly program with the flexibility to accommodate the needs of users performing end-state free energy calculations. The source code can be downloaded at http://ambermd.org/ with AmberTools, released under the GNU General Public License.
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Miller B. R. et al. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations // Journal of Chemical Theory and Computation. 2012. Vol. 8. No. 9. pp. 3314-3321.
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Miller B. R., Mcgee T. D., Swails J. M., Homeyer N., Gohlke H., Roitberg A. MMPBSA.py: An Efficient Program for End-State Free Energy Calculations // Journal of Chemical Theory and Computation. 2012. Vol. 8. No. 9. pp. 3314-3321.
Cite this
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TY - JOUR
DO - 10.1021/ct300418h
UR - https://doi.org/10.1021/ct300418h
TI - MMPBSA.py: An Efficient Program for End-State Free Energy Calculations
T2 - Journal of Chemical Theory and Computation
AU - Miller, Bill R
AU - Mcgee, T Dwight
AU - Swails, Jason M.
AU - Homeyer, Nadine
AU - Gohlke, H
AU - Roitberg, Adrian
PY - 2012
DA - 2012/08/16
PB - American Chemical Society (ACS)
SP - 3314-3321
IS - 9
VL - 8
PMID - 26605738
SN - 1549-9618
SN - 1549-9626
ER -
Cite this
BibTex (up to 50 authors)
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@article{2012_Miller,
author = {Bill R Miller and T Dwight Mcgee and Jason M. Swails and Nadine Homeyer and H Gohlke and Adrian Roitberg},
title = {MMPBSA.py: An Efficient Program for End-State Free Energy Calculations},
journal = {Journal of Chemical Theory and Computation},
year = {2012},
volume = {8},
publisher = {American Chemical Society (ACS)},
month = {aug},
url = {https://doi.org/10.1021/ct300418h},
number = {9},
pages = {3314--3321},
doi = {10.1021/ct300418h}
}
Cite this
MLA
Copy
Miller, Bill R., et al. “MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.” Journal of Chemical Theory and Computation, vol. 8, no. 9, Aug. 2012, pp. 3314-3321. https://doi.org/10.1021/ct300418h.