Hello, I want to derive the atomic partial charges for heme in chloroperoxidase, since these parameters cannot be found in the GROMOS53a6 force field. Chloroperoxidase is a cysteine-ligated heme protein (high spin) much like P450. In my work, I want to study the interactions between the protein residues of chloroperoxidase and its substrates. Thus, I used the QM software ORCA to optimize the heme-thiolate structure (TPSS/def2-SPVD), and then I used CHELPG method to derive the heme charges. Could anyone tell me if the method I used is suitable for my purpose?
In addition, the charges I obtained for Fe (0.931877) and nitrogen (-0.44572, -0.34427, -0.39467, and -0.39467) are largely consistent with two reference. The reference are one in 1995 (Fe: 1.0, N: -0.4; Helms et al. Thermodynamics of water mediating protein-ligand interactions in cytochrome P450cam: a molecular dynamics study, Biophys. J. 69: 810-24) and one in recent (Fe: 0.847, N: -0.37, -0.423, -0.504, and -0.528; Favia et al. (2006) Three-dimensional model of the human aromatase enzyme and density functional parameterization of the iron-containing protoporphyrin IX for a molecular dynamics study of heme-cysteinato cytochromes, Proteins 62: 1073-84). I will greatly appreciate any comment and suggestions. Best Regards, Rui -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
