If you're only trying to include 3 water molecules that you know are important, try the following:

1- Edit the pdb file of your template to only include these specific ones, i.e, delete all other water molecules. Number these two water molecules 515 516, and 517. 2- Edit your .top file deleting the WATER_IO = on command and leave the HETATM_IO = on command. 3- I usually use .pir and not .ali but this may still be applicable. Edit your .ali file as follows: (a) Change the second line in the paragraph so it will be: structureX:Bamu:1 : :517H : :unknown:unknown:-1.00:-1.00

(b) Remove the /w* at the end of the molecule from both template and your sequence lines. (c) After the last residue in the template, add XXX* that would correspond to the 3 water molecules in the pdb file. (d) After the last residue in the Sequence lines add ...* (e) Make sure that the XXX* in the template and the ...* align exactly right. It seems you will not have a problem with this since the alignment is rather simple. (f) Change the second line in the template paragraph to: sequence:CcHh1:1 : :523 : :unknown:unknown:-1.00:-1.00

I might be wrong but it seems like Modeler is confused about what is "w".

I hope it works!!

Best regards,

Walid Mohsen

Al-Walid A. Mohsen, Ph.D. Research Assistant Professor Department of Pediatrics School of Medicine University of Pittsburgh 3460 Fifth Ave, Rangos 2113 Pittsburgh, PA 15213 U.S.A. Phone: (412) 692-7928

> From: modeller_usage-request@salilab.org > Reply-To: modeller_usage@salilab.org > Date: Tue, 3 Jan 2006 02:52:59 -0800 > To: modeller_usage@salilab.org > Subject: modeller_usage Digest, Vol 5, Issue 2 > > Send modeller_usage mailing list submissions to > modeller_usage@salilab.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://salilab.org/mailman/listinfo/modeller_usage > or, via email, send a message with subject or body 'help' to > modeller_usage-request@salilab.org > > You can reach the person managing the list at > modeller_usage-owner@salilab.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of modeller_usage digest..." > > > Today's Topics: > > 1. modelling with ligands again! mainly water issues (jo hanna) > 2. Modelling with ligands - Not Working! (Joanne Hanna) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 3 Jan 2006 10:21:12 +0000 > From: jo hanna jfhanna@gmail.com > Subject: [modeller_usage] modelling with ligands again! mainly water > issues > To: modeller_usage@salilab.org > Message-ID: > 4b21263d0601030221y59eef18eo9a8fc712b6fe89d6@mail.gmail.com > Content-Type: text/plain; charset="iso-8859-1" > > 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 >