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'