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,