AMBER Archive (2005)

Subject: Re: AMBER: Protein with structural ions

From: Oliver Hucke (ohucke_at_u.washington.edu)
Date: Tue Apr 05 2005 - 16:42:29 CDT

Kara,

a straightforward method is the "bonded model" developed in the group of
K. Merz. If this is interesting for you, please have a look e.g. at:

@Article{70838,
   author = {S. C. Hoops and K. W. Anderson and K. M. Merz},
   title = {Force field design for metalloproteins},
   journal = {J. Am. Chem. Soc.},
   year = {1991},
   key = {metalloproteins ; force field development},
   volume = {113},
   pages = {8262-8270},
}

@Article{70863,
   author = {D. Suarez and E. N. Brothers and K. M. Merz},
   title = {Insights inton the structure and dynamics of the dinuclear
zinc $\beta$ lactamase site from {\sl bacteroides fragilis}},
   journal = {Biochemistry},
   year = {2002},
   key = {AMBER ; zinc enzyme ; bonded model ; method ; force field ;
QM/MM},
   volume = {41},
   pages = {6615-6630},
}

You basically would have to introduce covalent bonds between the
ligating side chains and the metal ion. For that purpose you need to
recalculate the partial charges of the metal plus the side chains bound
to it in order to model the charge transfer.

OLiver

________________________________________________________________

Oliver Hucke, Dr.
Biomolecular Structure Center Health Sciences Building - K418C
Dept. of Biochemistry 1959 NE Pacific St.
University of Washington phone: (206) 685 7046
Box 357742 fax : (206) 685 7002
Seattle, WA 98195-7742 email: ohucke_at_u.washington.edu
________________________________________________________________

Kara Wald wrote:
> I'm beginning to run a protein/inhibitor and noticed that after an
> initial minimization with implicint solvent, the structural zinc and
> calcium atoms seemed to "float" away from the protein. Is there a way
> to stop this in an uncomplicated way?
>
> Thanks,
>
> Kara Di Giorgio
>
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