------ Forwarded Message
From: Oliver Hucke <>
Date: Fri, 07 Mar 2003 10:00:39 +0100
To: Modeller Care <>
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
--
____________________________________________________________________________
Oliver Hucke
Inst. fuer Physikalische Chemie II
Universitaet Freiburg
Albertstr. 23a
D-79104 Freiburg
Tel. : +49-761-203-5130 (/-6179)
Fax. : +49-761-203-6189
email:
____________________________________________________________________________
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