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: 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 >