7 Dec
1998
7 Dec
'98
6:13 p.m.
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: sancher@rockvax.rockefeller.edu
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