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.
Your work sounds like you want a nonbonded metal force field parameter.
Try using frcmod.ions1lm_1264_tip3p
I have seen the frcmod.ionsjc_tip3p file in the following link:
https://github.com/choderalab/ambermini/blob/master/share/amber/dat/leap/parm/frcmod.ionsjc_tip3p
> And this force field file for monovalent ions. you have not mentioned which oxidation state you want (Fe2 or Fe3).
>Don't mix up the water model force field file using a different set of force fields. If you want TIP3P then only the same force field file you used or vice-versa for SPC/E.
Hopefully, it will work.
- Badges
- Science topic