Hello again
In follow up to my own question I have found that the issue only really occurs when i try to include the water, either with the other ligand or even without (after re ordering of the pdb file) Does the water in the pdb file have to have H atoms attached or is a crystallographic O sufficient?
My log with the hetatms only no water, is: 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__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 51172 47475
which still shows these atoms absent errors which i don't understand.
When adding just the water and no other ligand my top and aln files are appended and my log error is an out of bounds as before. SO it aapears that the water is the problem, I have also tried in my log file with only the water changing the line SET HETATM_IO = on, WATER_IO = on to just SET WATER_IO = on but this maks no difference.
delete__442E> One or more atoms absent from MODEL: O: 522: C: 522: N: 523: CA: 523: delete__443_> Restraints marked for deletion were removed. Total number of restraints before, now: 48782 45085 nselat__596E> Atom index is out of range (iatm,natm): 4009 4008 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1
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'\
ALIGNMENT >P1;Bamu structureX:Bamu:1::515::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::523::::0.00: 0.00 GPAERLELLAGWNDTDADRAR-PGLVEMFREQARARPDAVAVVDERRTLTYRQVEKLSAQLAHQLLARGLAVEDV VGISLERSAEMVIGLLAVLRAGGAFVPLDPHWPAERRAVVIEDAGVVVQLDASGEPAPG---EPEAVAVDLGDWR FGDRPTEDTGVTVPGDALAYVIFTSGSTGRPKGAMIRHEAISERLLWQIHEILGFGHDDASLFKAPLSFDISINE IFLPLVSGGRLVVLRPGGERDPHHLLSVIDEQRVTFTYLVSSMLDVLLEMAGDSGRLDSLRHVWCGGEVLTPELY ERFRTRLDIPLYHGYGPAETTIGVSHVVYRGAAERLSTSIGRANPNTRLYVLDDELRPVPVGVGGELYAGGLLLG RGYVNAPGLTASRFVANPFADDGSRLYRTGDLARFAPDGSLDFLGRADNQVKIRGMRLEIEDVEVGLAEHPRVRH TCVVARKNTAGGTYLVGYVIPAAGHEDLRADEVKAWAGEHMVEYMVPTHVVVMTEFPLTANGKLDRNALPEPVIP A/w*
Sorry to post so many mails, I'm really struggling to figure this out!
Jo