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January 2006

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Modelling with ligands - Not Working!
by Joanne Hanna 02 Jan '06

02 Jan '06

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 J.F.Hanna(a)warwick.ac.uk

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