dear charmm users:
i am looking charmm parameters for 4- and 5-coordinated hemes. i am trying to simulate this protein, in which there are several hemes, some of the 5-coordinated hemes, so I am looking 5-coordinated heme parameters. i saw a post in this forum, that stated there is no parameter like that, if this is the case what is the way proceed? it was mentioned that old parameters may have something, how could I take a look at that?
the second question I have is about 4-coordinated hemes, one of the hemes in the protein does not have any ligand to except that water molecule is proposed (resolution is not high enough to see clearly) that there is water molecule provides the ligand to the iron of the heme, so I am trying to test it, however i do not know how good it be if i do not have reasonable parameters for this heme.
Of course, if one use six liganded heme parameters, heme iron collapses to the oxygen of the water, so i got to apply some lennard-jones parameters to the iron, so I am wondering about that?
Any help is appreciated.
Thanks, Nara
