Greetings Forum users I have a problem with adding Calcium ions in my models. I'm using this TOP script:
#Homology modelling by the MODELLER TOP routine 'model'.
INCLUDE # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = '23urom-1lmj.ali' # alignment filename SET KNOWNS = '1lmjA' # codes of the templates SET SEQUENCE = '23urom' # code of the target SET ATOM_FILES_DIRECTORY = '/net/rossini/mesana/PROVA_MODELLER/MODELING_CALCIUM/1lmj.atm' # directories for input atom files SET HETATM_IO = ON SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 10 # index of the last model # (determines how many models to calculate)
CALL ROUTINE = 'model' # do homology modelling
And this is my alignment: >P1;1lmjA structureX:1lmj.pdb: 3 :A:+88 :A:undefined:undefined:-1.00:-1.00 TDIDECRISP--DLCGRGQCVNTPGDFECKCDEGYESGFMMMKNCMDIDECQRDPLLCRGGVCHNTEGSYRCECP PGHQLSPNISACI33*
>P1;23urom sequence:phd2: : : : ::: 0.00: 0.00 -DLDECAIPGAHNCSANSSCVNTPGSFSCVCPEGFRLSPGLGCTDVDECAEPGLSHCHALATCVNVVGSYLCVCP AGYRGD--GWHCE33*
The models generated by MODELLER contain the ions: ATOM 603 OXT GLU 85 14.608 -30.221 -12.881 1.00 30.85 1SG 604 TER 603 GLU 85 1SG 605 HETATM 604 CAL CAL 86 22.805 -57.972 -18.845 1.00 0.00 1SG 606 HETATM 605 CAL CAL 87 -43.926-115.000-182.203 1.00 0.00 1SG 607 END
But the position of these Calcium ions is completely wrong, outside of the molecule and differing from the template. How can I solve this problem? Many thanks in advance for your help,
Lella Sana wrote: > I have a problem with adding Calcium ions in my models. > I'm using this TOP script: ... > The models generated by MODELLER contain the ions: > ATOM 603 OXT GLU 85 14.608 -30.221 -12.881 1.00 30.85 1SG 604 > TER 603 GLU 85 1SG 605 > HETATM 604 CAL CAL 86 22.805 -57.972 -18.845 1.00 0.00 1SG 606 > HETATM 605 CAL CAL 87 -43.926-115.000-182.203 1.00 0.00 1SG 607 > END > > But the position of these Calcium ions is completely wrong, outside > of the molecule and differing from the template. How can I solve this > problem?
Your script and alignment look OK to me. My best guess is that you're using an old version of Modeller with a new template PDB file (post remediation). (The post-remediation calcium ion is called "CA" but old versions of Modeller called it "CAL".) Modeller will only inherit coordinates from templates if the atom names match. Does your PDB file call the calcium atoms "CA" or "CAL" ? If "CA" (which is what it should be these days) the best solution is to upgrade Modeller to the latest release, 9v5, which uses remediated residue and atom names. If for some reason you can't do that, you can either change your alignment to use '.' rather than '3', since BLK residues work just fine for ions and don't care about atom names, or you could possibly rename the calcium atoms and residues in your template PDB to "CAL".
Ben Webb, Modeller Caretaker
participants (2)
-
Lella Sana -
Modeller Caretaker