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In-House Software

Software for constant-pH molecular dynamics simulations

Constant-pH MD simulations allow the protonatable groups in a protein to change their protonation state during the simulations in a way that reflects the solution pH [Baptista 1997, Baptista 2002]. Check the corresponding webpage [link coming soon].

 

Software for proton and/or electron titration using a single protein structure

meadTools [download]
This is a set of software tools useful to run binding simulations of electrons and protons [Baptista 1999, Teixeira 2002], using proton tautomers [Baptista 2001, Teixeira 2002] or not, based on Poisson-Boltzmann (PB) calculations. It can be used to create the input to PETIT or MCRP (see below), assuming that the PB calculations are done using the MEAD package by Donald Bashford. Some tools depend also on GROMACS and ASC.
PETIT [download]
General program for systems with multiple-state sites. The typical use of the program is the treatment of proton configurations [Baptista 2001, Teixeira 2002], which includes the protonation of sites with proton tautomerism, and the orientation of hydroxyl and thiol groups (Ser, Thr, Cys) and water molecules. (Note that PETIT can be used outside of the context of protonation and/or redox equilibrium, such as to perform conformational sampling of side-chain conformations, but in such a case the required structural energy terms cannot be obtained using meadTools.)
MCRP [download]
This program is intended for systems with two-state sites only [Baptista 1999]. It is much faster than PETIT in this particular case, because extensive optimizations can be done.

 

GROMACS-4.0.7-ionstr : GRF with ionic strength as an external parameter

The implementation of the generalized reaction field (GRF) method [Tironi 1995] in GROMACS uses the charges of the system to automatically determine an ionic strength value that is used by the method. We have introduced a simple modification in GROMACS [Machuqueiro 2006] that takes instead the ionic strength as an external parameter given in the .mdp file, like the temperature or the pressure. [download]

 

GROMOS 54A7 force field for GROMACS

This is a package containing the files required to run simulations in GROMACS using the GROMOS 54A7 force field [Schmid 2011]. The files were built in collaboration with the Protein Modelling Lab of ITQB/UNL. [download]

 

References

Baptista, A. M., Martel, P. J., Petersen, S. B. (1997) Simulation of protein conformational freedom as a function of pH: constant-pH molecular dynamics using implicit titration. Proteins, 27:523-544.

Baptista, A. M., Martel, P. J., Soares, C. M. (1999) Simulation of electron-proton coupling with a Monte Carlo method: Application to cytochrome c3 using continuum electrostatics. Biophys. J. 76:2978-2998.

Baptista, A. M., Soares, C. M. (2001) Some theoretical and computational aspects of the inclusion of proton isomerism in the protonation equilibrium of proteins. J. Phys. Chem. B, 105:293-309.

Baptista, A. M., Teixeira, V. H., Soares, C. M. (2002) Constant-pH molecular dynamics using stochastic titration. J. Chem. Phys. 117:4184-4200.

Machuqueiro, M., Baptista, A. M. (2006) Constant-pH molecular dynamics with ionic strength effects: protonation-conformation coupling in decalysine. J. Phys. Chem. B, 110:2927-2933.

Schmid, N., Andreas, P. E., Choutko, A., Riniker, S., Winger, M., Mark, A. E., van Gunsteren, W. F. (2011) Definition and testing of the GROMOS force-field versions 54A7 and 54B7. Eur. Biophys. J. 40:843-856.

Teixeira, V. H., Soares, C. M., Baptista, A. M. (2002) Studies of the reduction and protonation behavior of tetraheme cytochromes using atomic detail. J. Biol. Inorg. Chem. 7:200-216.

Tironi, I. G., Sperb, R., Smith, P. E., van Gunsteren, W. F. (1995) A generalized reaction field method for molecular-dynamics simulations. J. Chem. Phys. 102:5451-5459.

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