Parameterisation of Metallo-protein with amber?

General Topics in Molecular Dynamics
1

Can someone please help me with a protocol for parameterizing a metallo-protein for MD simulation with amber forcefield? My protein has two FE molecules and the I tried using either frcmod.ionsjc_tip3p or frcmod.ions234lm_126_spce to generate topology but the system is not minimizing. I confirmed that there are no atomic clashes in my system, so I guess the problem has to do with the ions parameters.

2

Hi,

this is not a straightforward process. Please take a look at the Amber advanced tutorial to find out more about how to prepare a system involving metal ions.

Hope it helps.

1 Like
3

Hi adanazumi,

I would strongly suggest that you have a look at CHARMM-GUI https://charmm-gui.org (Solution builder) Despite the name, it is quite capable of generating amber files for even the most complex systems, as it has an extensive ion parameter library (I’ve recently used it for Mn2+ ions)

Hope this helps!

Kind regards,

S

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4

Thank you for your suggestion. I will check out!

5

Thank you very much. I will check out!