[modeller_usage] Modelling with ligands - Not Working!

["Joanne Hanna" <>]

Hello

I have been using modeller for some time now but have only recenetly
tried to produce a model including ligands and I am having some
difficulties (I am using 7v7, and therefore the top scripts). I would
really appreciate some help or advice!

The tutorial suggests that in order to include ligands in the modelling
process:

Manually alter alignment to take account of 'block' (in this case AMP,
Mg and one H2O).
e.g. i have added /..w* at end of template and target in *.ali alignment
file

Then use this alignment, together with a pdb containing the
ligands/cofactors/water to produce a model containing the ligands.
including the hetatm and water in the top file.

This doesn't seem to work for me however. I have to change the number of
residues in the alignment file from 514 to 517 to take account of the 3
'ligands' and when i run my model.top scripts (see below) i get the
following failure:

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

I know that my alignment is not brilliant in the region 134-138 but it
is the other errors that are puzzling me. I particularly don't
understand the range error as i have 4142 atoms in my pdb file. And
there are no atoms missing from my pdb file as I have rebuilt all
missing atoms from the inital pdb using the modeller loop routine.

Can anyone suggest how to fix this, or indeed tell me if the procedure
that i have gone through is correct?In addition to this in the alignment
file the -1.00:-1.00 part, is this correct?

Many thanks in advance for any help/suggestions!

Jo

alignment file (after modeification of /..w and 517 residues in
structure):
>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*

top script:

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'

Joanne Hanna
Department of Chemistry
University of Warwick
Coventry
CV4 7AL