Dear Marco,
It is possible to restrain any kind of spatial restraint (angle, distance etc.)
in Modeller, using external data from experimental results (additional NMR
constraints) or some preliminary knowledge as in your case.
e.g. in your case you can introduce distance restraints among the three
residues. the easiest way is to include in your top file a redefined
SPECIAL_RESTRAINTS routine, with the desired values and parameters.
I include an example below, which restrains 2 distances between atoms of
residues 166 and 336 and 191 and 336.
For the details of the parameters, please look up the manual.
####################
SUBROUTINE ROUTINE = 'special_restraints'
ADD_RESTRAINT ATOM_IDS = 'NH1:166' 'O1:336',;
RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1
ADD_RESTRAINT ATOM_IDS = 'NE2:191' 'O4:336',;
RESTRAINT_PARAMETERS = 2 1 1 22 2 2 0 3.5 0.1
RETURN
END_SUBROUTINE
#################
Andras
MarcoBocola wrote:
>
> Hello from Marburg,
>
> I want to do homology modelling on serine hydrolases with highly
> conserved
> fold and reasonable AA-identity.
> So the difficulty is to model the active site correctly with respect to
> the catalytic triade and the backbone nitrogens in the oxyanion hole.
>
> These few amino acids should be overlayed as exact as possible.
>
> Is there a straightforward way to contstrain modeller only for these
> higly conserved topology of the catalytic residues within one Angstroem,
> thus remaining the catalytic hydrogen bond network intact.
>
> Any hints on possible protocolls appreciated.
>
> Marco
--
,
Andras Fiser, PhD # phone: (212) 327 7216
The Rockefeller University # fax: (212) 327 7540
Box 270, 1230 York Avenue # e-mail:
New York, NY 10021-6399, USA # http://salilab.org/~andras