Hi Roberto
Thanks for the advice. Unfortunately it's clear symmetry is not
operating. In the log file I get
defsym___> New number of symmetry segments, atom pairs: 1 0
but then in the energy output
Value of the symmetry term within -Ln(Mpdf) : 0.00000E+00
Any other ideas?
Daniel Rigden
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On Mon, 7 Dec 1998, Roberto Sanchez wrote:
> Hi,
>
> Your TOP file looks fine to me. If the symmetry is operating you should
> get a value that is different from 0.0000 in the following line in the
> log file:
>
> Value of the symmetry term within -Ln(Mpdf) : 0.0000
>
> just grep for "symmetry" and you will get the line.
>
> By the way, you don't need to (and maybe you shouldn't) edit the
> __special.top script. It is enough to redefine a subroutine in your main
> TOP file. You can just add the code you show to your main TOP file and
> the new 'special_restraints' routine will be used by MODELLER.
>
> I hope this helps.
>
> Best Wishes,
>
> Roberto
>
> --
> Roberto Sanchez | phone : (212) 327 7206
> The Rockefeller University | fax : (212) 327 7540
> 1230 York Avenue, Box 38 | e-mail:
> New York, NY 10021-6399 | http://salilab.org
>
>
> Daniel John Rigden wrote:
> >
> > Dear Modellers
> >
> > I'm trying to build a dimer, constraining the two monomers to be
> > identical. From the manual this seems reasonably straightforward but I
> > can't get it to work.
> >
> > My current idea is to include the commands in the 'special_restraints'
> > subroutine (in __special.top), which gets called by __homscr.top after the
> > other restraints subroutines, thus
> >
> > SUBROUTINE ROUTINE = 'special_restraints'
> >
> > # Try to put symmetry restraints here
> > # This is called from __homcsr after other restraints set up
> >
> > SET ATOM_TYPES = 'ALL'
> > SET SELECTION_STATUS = 'INITIALIZE'
> > SET SELECTION_SEARCH = 'SEGMENT'
> >
> > SET SYMMETRY_WEIGHT = 5.0
> > PICK_ATOMS PICK_ATOMS_SET = 2, SELECTION_SEGMENT = '1:' '89:'
> > PICK_ATOMS PICK_ATOMS_SET = 3, SELECTION_SEGMENT = '90:' '178:'
> > DEFINE_SYMMETRY ADD_SYMMETRY = on off
> >
> > RETURN END_SUBROUTINE
> >
> > I know that this subroutine is read but I never see any indication of
> > symmetry having been set up when I read the logfile.
> >
> > What am I doing wrong?
> >
> > Thanks in advance
> >
> > Daniel Rigden
>