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'