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[modeller_usage] Problems with modelling with ligand



Hello

I apologise if this message is posted more than once, I am having difficulties with my email system.

My questions regards the process for modelling with ligands.

>From the tutorial i understand that you have the ligands in the pdb file template and then you manually alter the alignment to take account of these ligands, for me that means adding /..w* to the end of the structure and seqeunce alignments (i'm unsure if you add it to the seqeunce, if you want it included). This also means changing the number of residues in the structure file in the alignment to include the 3 BLK/water items, as even if they are included in the pdb prior to alignment they are not included in the residue number line in the alignment (i.e. in alignment below changing original 514 to 517).

I then do the modelling using the alignment, as appended below and the model.top script (7v7 user!) also below and get the following error which i do not understand.

check_ali___> Checking the sequence-structure alignment.

Implied target CA(i)-CA(i+1) distances longer than  8.0 angstroms:

ALN_POS  TMPL  RID1  RID2  NAM1  NAM2     DIST
----------------------------------------------
    134     1  134   138      G     E    8.407
END OF TABLE


delete__442E> One or more atoms absent from MODEL:  O: 522: C: 522: N: 523: CA: 523:
delete__442E> One or more atoms absent from MODEL:  O: 523: C: 523: N: 524: CA: 524:
delete__442E> One or more atoms absent from MODEL:  O: 524: C: 524: N: 525: CA: 525:
delete__443_> Restraints marked for deletion were removed.
              Total number of restraints before, now:    51247    47550
nselat__596E> Atom index is out of range (iatm,natm):     4033     4032
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

Dynamically allocated memory at          finish [B,kB,MB]:     26700639   26074.844    25.464
Starting time                                            : 2006/01/02  21:50:15.029
Closing time                                             : 2006/01/02  21:50:35.218
Total CPU time [seconds]                                 :      20.18
 
I unerstand distance table and know which region of my alignment this points to but I do not understand the missing atoms or the out of range error, as I have 4142 atoms and no missing atoms. Could anyone help with where I am going wrong?! And also tell me if my procedure is correct, should the alignment automatically include the 3 BLK/water residues in the resdiue number if it is in the pdb file? and if i want the ligands in the output model is it correct to state /..w* at the end of this sequence in the alignment too? Also in the alignment is it correct for the seqeunce line to read: sequence:CcHh1:     : :     : :::-1.00:-1.00 ?

Any feedback would be greatly appreciated.

Thanks
Jo

ALIGNMENT
>P1;Bamu
structureX:Bamu:   1 : : 517 : :undefined:undefined:-1.00:-1.00
GTHEEEQYLFAVNNTKAEYPRDKTIHQLFEEQVSKRPNNVAIVCENEQLTYHELNVKANQLARIFIEKGIGKDTL
VGIMMEKSIDLFIGILAVLKAGGAYVPIDIEYPKERIQYILDDSQARMLLTQKHLVHLIHNIQFNGQVEIFEEDT
IKIREGTNLHVPSKSTDLAYVIYTSGTTGNPKGTMLEHKGISNLKVFFEN-SLNVTEKDRIGQFASISFDASVWE
MFMALLTGASLYIILKDTINDFVKFEQYINQKEITVITLPPTYVVHL-----DPERILSIQTLITAGSATSPSLV
NKWKE--KVTYINAYGPTETTICATTWVATKETIGHSVPIGAPIQNTQIYIVDENLQLKSVGEAGELCIGGEGLA
RGYWKRPELTSQKFVDNPFVP-GEKLYKTGDQARWLSDGNIEYLGRIDNQVKIRGHRVELEEVESILLKHMYISE
TAVSVHKDHQEQPYLCAYFVSE---KHIPLEQLRQFSSEELPTYMIPSYFIQLDKMPLTSNGKIDRKQLPEPDLT
F/..w*

>P1;CcHh1
sequence:CcHh1:     : :     : :::-1.00:-1.00
GPAERLELLAGWNDTDADRAR-PGLVEMFREQARARPDAVAVVDERRTLTYRQVEKLSAQLAHQLLARGLAVEDV
VGISLERSAEMVIGLLAVLRAGGAFVPLDPHWPAERRAVVIEDAGVVVQLDASGEPAPG---EPEAVAVDLGDWR
FGDRPTEDTGVTVPGDALAYVIFTSGSTGRPKGAMIRHEAISERLLWQIHEILGFGHDDASLFKAPLSFDISINE
IFLPLVSGGRLVVLRPGGERDPHHLLSVIDEQRVTFTYLVSSMLDVLLEMAGDSGRLDSLRHVWCGGEVLTPELY
ERFRTRLDIPLYHGYGPAETTIGVSHVVYRGAAERLSTSIGRANPNTRLYVLDDELRPVPVGVGGELYAGGLLLG
RGYVNAPGLTASRFVANPFADDGSRLYRTGDLARFAPDGSLDFLGRADNQVKIRGMRLEIEDVEVGLAEHPRVRH
TCVVARKNTAGGTYLVGYVIPAAGHEDLRADEVKAWAGEHMVEYMVPTHVVVMTEFPLTANGKLDRNALPEPVIP
A/..w*

MODLE.TOP

INCLUDE
SET ALNFILE = 'CcHh1-Bamu.ali'
SET KNOWNS = 'Bamu'
SET SEQUENCE = 'CcHh1'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 1
SET HETATM_IO = ON, WATER_IO = ON
CALL ROUTINE = 'model'