------ Forwarded Message From: Oliver Hucke Oliver.Hucke@physchem.uni-freiburg.de Date: Fri, 07 Mar 2003 10:00:39 +0100 To: Modeller Care modeller-care@salilab.org Subject: Re: Protein+Metal Ion?
Dear Marc,
you might define the subroutine 'special_restraints' at the end of your top script introducing the bonds between the metal ligand atoms and the metal atom in form of e.g. harmonic potentials. In my case the following introduced 6 ligand-Fe bonds:
SUBROUTINE ROUTINE = 'special_restraints' SET ATOM_IDS 'NE2:501' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'NE2:541' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'NE2:815' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'NE2:862' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'OE1:830' 'FE2:1185' ADD_RESTRAINT RESTRAINT_PARAMETERS = 3 1 1 27 2 2 0 2.2 0.1 SET ATOM_IDS 'OE2:830' 'FE2:1185' RETURN END_SUBROUTINE
Note: the numbers of the residues correspond to the modeller numbering scheme. You may get the correct numbers from an *.ini file.
Info on the meaning of the ADD_RESTRAINT lines can be found in the chapter "specification of restraints" in the modeller manual
Hope this helps! Best,
Oliver
> I would like to model a protein that contains Zn in the active site. In = > the template structure, two His residues are coordinated to the Zn. The = > target sequence also has these residues and the sequences display > 50% = > identity. How do I force the His residues to similarly coordinate the = > Zn in the modelled structure? If the Zn atom is in .pdb file, modeller = > doesn't seem to notice. Without the Zn atom present, the His = > sidechains simply flop around in the active site (not surprisingly). > > Marc Campitelli