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
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
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
+-------------------------------------------------------------------------+ | Dr Daniel Rigden | | CENARGEN/EMBRAPA | e-mail: daniel@cenargen.embrapa.br | | S.A.I.N. Parque Rural, Final W5 | http://www.cenargen.embrapa.br | | Asa Norte | Phone: +55 (61)340-3550 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3624 | +-------------------------------------------------------------------------+
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 >
Hi Roberto
I think I have the answer to the symmetry problem. With a more detailed log file I found that that RES_TYPE it was searching was BLK, a hangover from some previous step. If I insert
SET RES_TYPES = 'ALL'
I get
defsym___> New number of symmetry segments, atom pairs: 1 686
and then at the end
Value of the symmetry term within -Ln(Mpdf) : 17.403
So it worked, but I was surprised to find that the stereochemical quality of the constrained model is dreadful compared to that calculated without symmetry.
Anyway, another small question. At the moment my two monomers come out as residues 1-89 and 90-178, no chain ID. Is there any way to get them as 1-89 of chains A and B, say?
Thanks Daniel Rigden
+-------------------------------------------------------------------------+ | Dr Daniel Rigden | | CENARGEN/EMBRAPA | e-mail: daniel@cenargen.embrapa.br | | S.A.I.N. Parque Rural, Final W5 | http://www.cenargen.embrapa.br | | Asa Norte | Phone: +55 (61)340-3550 | | 70770-900, Brasilia-D.F.-BRAZIL | Fax: +55 (61)340-3624 | +-------------------------------------------------------------------------+
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 >
Hi
> > Anyway, another small question. At the moment my two monomers come out as > residues 1-89 and 90-178, no chain ID. Is there any way to get them as > 1-89 of chains A and B, say? > > Thanks > Daniel Rigden
That is very easy, look at the RENAME_SEGMENTS command in the manual. You should read in, rename and write out the sequence segments in question, with optional chain identifiers and new residue numbering.
Andras
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Andras Fiser -
Daniel John Rigden -
Roberto Sanchez