Parameterisation of Metallo-protein with amber · Biostar

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Parameterisation of Metallo-protein with amber

Hello guys!

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.

metallo-protein amber md ion simulation fe

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updated 4.3 years ago by Pappu

• written 4.3 years ago by Ammar Danazumi •

You could try to use gromacs.

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written 4.3 years ago by Pappu

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