Dear experts,
I need to perform MM-PBSA calculations using g_mmpbsa package. My problem is that how to determine proper parameters for .mdp file. for example Solute dielectric constant (pdie) or PBsolver.
Any help will be greatly appreciated.
Regards,
Farideh
You can use gromacs program (www.gromacs.org) to create the topology file with force field parameters. For the solute dielectric constant usually is considered as free parameter, typically between 2-16 (but you should try different values in this range; some, for example Warshel group, (http://laetro.usc.edu/) even suggest to be distance dependence and not just a constant), however, it can also be estimated from the fluctuations of the total dipole momentum of protein.
Dear Dr. Hiqmet Kamberaj
Thanks for your time and support.
Regards,
Farideh
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