Cite xBFreE

If you found gmx_MMPBSA useful for your research, please cite:

Valdés-Tresanco, M.S., Valdés-Tresanco, M.E., Valiente, P.A. and Moreno E. gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACS. Journal of Chemical Theory and Computation, 2021 17 (10), 6281-6291. https://pubs.acs.org/doi/10.1021/acs.jctc.1c00645. Download | *.bib | *.ris

Please also consider citing MMPBSA.py's paper:

Bill R. Miller, T. Dwight McGee, Jason M. Swails, Nadine Homeyer, Holger Gohlke, and Adrian E. Roitberg. MMPBSA. py: An Efficient Program for End-State Free Energy Calculations. Journal of Chemical Theory and Computation, 2012 8 (9), 3314-3321. https://pubs.acs.org/doi/10.1021/ct300418h. Download | *.bib | *.ris | *.xml

Example¶

Here there is an example on how to cite gmx_MMPBSA and programs/methods implemented in it:

MM/GBSA calculations

PBC conditions were removed from GROMACS output trajectory before running the calculations with gmx_MMPBSA.^1,2 Energetically relevant residues within 5 Å at the interface were predicted using the per-residue effective free energy decomposition (prEFED) protocol.³ The AMBER99SB force field⁵ was used to calculate the internal term (ΔE_int) as well as van der Waals (ΔE_vdW) and electrostatic (ΔE_ele) energies. The GB-Neck2 model (igb = 8)⁶ was used to estimate the polar component of the solvation energy (ΔG_GB) while the non-polar solvation free energy (∆𝐺_𝑆𝐴) was obtained by the equation:

∆𝐺_𝑆𝐴 = 𝛾 · ∆𝑆𝐴𝑆𝐴 + 𝛽

where ∆𝑆𝐴𝑆𝐴 represents the solvent-accessible surface area variation of the solute molecule upon complex formation, and 𝛾 and 𝛽 are empiric constants whose values for GB models are 0.0072 kcal·Å^-2·mol^-1 and 0, respectively.^7,8 The entropic term was calculated by the Interaction Entropy method.⁹ The input file for gmx_MMPBSA decomposition calculation is shown below:

============================
Sample input file with decomposition analysis
&general
startframe=1750, endframe=2400, interval=1, PBRadii=4,
forcefields="oldff/leaprc.ff99SB"
/
&gb
igb=8, saltcon=0.150, intdiel=5,
/
&decomp
idecomp=2, dec_verbose=3,
print_res="within 5"
============================

Computational alanine scanning¹⁰ was performed for five residues (TP62, EP68, EP70, HP76, and EP83) with a specific internal dielectric constant as suggested by Yan et al.¹¹ and according to the chemical-physical properties of the mutated amino acid (i.e., e_i = 5 for charged residues; e_i = 3 for polar residues; and e_i = 1 for hydrophobic residues). An example of the input file for gmx_MMPBSA alanine scanning (EP68 residue) calculation is shown below:

============================
Sample input file for alanine scanning analysis
&general
startframe=1750, endframe=2400, interval=1, PBRadii=4,
forcefields="oldff/leaprc.ff99SB", interaction_entropy=1, ie_segment=25, temperature=298
/
&gb
igb=8, saltcon=0.150,
/
&alanine_scanning
mutant='ALA', mutant_res='C:68', cas_intdiel=1
/
============================

Authors¶

• Mario Sergio Valdés Tresanco, PhD Student. University of Medellin, Colombia
• Mario Ernesto Valdés Tresanco, PhD Student. University of Calgary, Canada.
• Pedro Alberto Valiente, PhD. University of Toronto, Canada
• Ernesto Moreno Frías, PhD. University of Medellin, Colombia