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Poltype 2: Automated Parameterization and Free Energy Prediction for AMOEBA
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the parameter of the heme cofactor in Its ferrous and ferric Forms #35

Open Cynthia-0807 opened 1 year ago

Cynthia-0807 commented 1 year ago

Can poltype2 generate the parameter of the heme cofactor in Its ferrous and ferric Forms? As shown below(Fe3+ is six-coordinated, and binds to residue CYS）: image

jacekkozuch commented 1 year ago

Hi, before the Poltype ppl respond, you may be interested in this paper, where ferrous and ferric heme were paramterized: 'AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms': https://pubs.acs.org/doi/10.1021/acs.jctc.7b01128

Maybe I'm not up to date, but I think Poltype2 is more organic molecule-focused and cannot handle metals and their complexes automatically. If you want to get parameters for the oxoferryl compound as shown in the figure, then you could start from the valence parameters in the paper above. Then you would have to add/modify the 'polarize', 'vdw', 'bond', 'angle' etc involving the Fe=O part appropriately. This you may have to do 'manually' and consistent to the rest of the parameter set. That's something that would involve some considerable amount of fitting the parameters against QM calculations. Getting the 'multipoles' is then rather simple using POTENTIAL function in TINKER.

Unfortunately, I don't think that there's any tutorial on how to do that step by step, since the tutorials on the TinkerTools homepage are not around anymore.

Cynthia-0807 commented 1 year ago

Hi, before the Poltype ppl respond, you may be interested in this paper, where ferrous and ferric heme were paramterized: 'AMOEBA Polarizable Force Field Parameters of the Heme Cofactor in Its Ferrous and Ferric Forms': https://pubs.acs.org/doi/10.1021/acs.jctc.7b01128

Maybe I'm not up to date, but I think Poltype2 is more organic molecule-focused and cannot handle metals and their complexes automatically. If you want to get parameters for the oxoferryl compound as shown in the figure, then you could start from the valence parameters in the paper above. Then you would have to add/modify the 'polarize', 'vdw', 'bond', 'angle' etc involving the Fe=O part appropriately. This you may have to do 'manually' and consistent to the rest of the parameter set. That's something that would involve some considerable amount of fitting the parameters against QM calculations. Getting the 'multipoles' is then rather simple using POTENTIAL function in TINKER.

Unfortunately, I don't think that there's any tutorial on how to do that step by step, since the tutorials on the TinkerTools homepage are not around anymore.

Thanks for your suggest.I will read the reference you mentioned carefully and search the process of parameterization.