I want to dock some compounds as an inhibitors for hCAII. The purpose is to find some pharmacophoric features to build qualitative pharmacophore model and also I want to use GOLD for docking. Is it possible to use CHARMM forcefield for optimizing my enzyme? it has Zn in its catalytic active site. I want to know that CHARMM is compatible with zinc or not?
I'm really appreciate if anybody could help me. thanks
Yup CHARMM forcefield can be used. It has parameters for Zn+2.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2676146/
It is better to use CHARMM22.
Follow the reference: http://springer.libdl.ir/article/10.1007/s10822-010-9409-6
Hi Yeganeh,
Follow the below link for your clarification regarding the Forcefield for Zinc.
https://www.researchgate.net/post/Does_anyone_have_any_idea_where_I_can_get_zinc_force_field_parameter_without_dummy_atoms
Here are two articles which uses CHARMM & AMBER respectively.
Based on your system (Protein) you can select any of the used Forcefields.
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2818142/
http://pubs.acs.org/doi/abs/10.1021/j100028a030
Cheers!!
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