Dear Researchers,
I wanna calculate harmonic potential bond (bond length(r0), force constant(k)) and Lj parameters via a computational method for MTE-MOS complex's which contains a Mo in (pdb ID: 3nvy) for molecular dynamics simulation by Gromacs . But I don’t know how to calculate them.Would you please guide me that how can I get/calculate them?
Sincerely
M. Bagheri
I think you can use Automatic topology builder web server to generate parameters for Mo.
For Mo you have to search literature; if you find it then good. You just need sigma and epsilon value for it which you have to change in nonbonded itp file of your selected force field.
You have to use Ab initio calculations using softwares like Gaussian in order to obtain that parameters.
First, You have to perform ab-inito calculation using software like Gaussian, GAMESS and Turbomole, and calculate the equilibrium bond length, angle and torsion angle. Then u have to perform PES to collect the bonded potentials and then u have to fit it using polynomial function. The order of function you have to select manually. You can perform ESP and superamolecular approach to calculate the electrostatic and LJ potentials.
You can contact me for any further discussion.
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