I have designed mutants that should form dimers in a solution (or at least in crystal structure) using tetraedric or octaedric cobalt coordination and I am trying to compare their affinities computationally using NAMD.
I am not that experienced in MD and was also unable to find parameters that would include cobalt and its coordination and am not sure how representative somehing like zinc would be. Can anyone point me to a way of simulating said dimers using NAMD or a reasonably approachable alternative?
Do a literature search for cobalt and its coordination parameters and add them to the force field parameter file.
Article Parameters for the AMBER force field for the molecular mecha...
Thank you for your response. For now i have been using CHARMM and have already found parameters for cobalt but some other common ions like zinc were different to my main parameters file. This made me concerned with the validity of joining parts of different parameter sets, since they might have been developed differently.
I will look into using the AMBER force field with cobalt parameters.
The protein by itself normally doesn't form dimers but i found highly related crystal structure in the same orientation.
The idea was to try to follow the structure od the pre-set dimer, where non-mutated should dissociate over time and mutants should not or at should at least last longer.
Granted I have already noticed that even wt stays and even jumps back together during first ~0.5ns of the 10ns runs (all atom, explicit solvent, charmm, namd, i think that incorrect solvation between the units might be the cause) which made me reconsider my approach. This is my secondary issue to the already mentioned question of using correct cobalt parameters.
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