- modeller_usage - salilab.org

Re: Adding water molecules as ligands (minor corrections); modeller_usage Digest, Vol 5, Issue 3
by Mohsen, Al-Walid 03 Jan '06

03 Jan '06

Please note the corrections below: Best regards, Walid > > Today's Topics: > > 1. Re: modeller_usage Digest, Vol 5, Issue 2 (Mohsen, Al-Walid) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 03 Jan 2006 11:09:35 -0500 > From: "Mohsen, Al-Walid" <mohsaw(a)chp.edu> > Subject: [modeller_usage] Re: modeller_usage Digest, Vol 5, Issue 2 > To: <modeller_usage(a)salilab.org> > Message-ID: <BFE00BEF.2014%mohsaw(a)chp.edu> > Content-Type: text/plain; charset="US-ASCII" > > 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 three 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 (model) 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 (model) lines add ...* > (e) Make sure that the XXX* in the template and the model ...* 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(a)salilab.org> >> Reply-To: <modeller_usage(a)salilab.org> >> Date: Tue, 3 Jan 2006 02:52:59 -0800 >> To: <modeller_usage(a)salilab.org> >> Subject: modeller_usage Digest, Vol 5, Issue 2 >> >> Send modeller_usage mailing list submissions to >> modeller_usage(a)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(a)salilab.org >> >> You can reach the person managing the list at >> modeller_usage-owner(a)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(a)gmail.com> >> Subject: [modeller_usage] modelling with ligands again! mainly water >> issues >> To: modeller_usage(a)salilab.org >> Message-ID: >> <4b21263d0601030221y59eef18eo9a8fc712b6fe89d6(a)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 >>

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Re: modeller_usage Digest, Vol 5, Issue 2
by Mohsen, Al-Walid 03 Jan '06

03 Jan '06

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(a)salilab.org> > Reply-To: <modeller_usage(a)salilab.org> > Date: Tue, 3 Jan 2006 02:52:59 -0800 > To: <modeller_usage(a)salilab.org> > Subject: modeller_usage Digest, Vol 5, Issue 2 > > Send modeller_usage mailing list submissions to > modeller_usage(a)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(a)salilab.org > > You can reach the person managing the list at > modeller_usage-owner(a)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(a)gmail.com> > Subject: [modeller_usage] modelling with ligands again! mainly water > issues > To: modeller_usage(a)salilab.org > Message-ID: > <4b21263d0601030221y59eef18eo9a8fc712b6fe89d6(a)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 >

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modelling with ligands again! mainly water issues
by jo hanna 03 Jan '06

03 Jan '06

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

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Problems with modelling with ligand
by jo hanna 03 Jan '06

03 Jan '06

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'

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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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out_put directory
by doppelt olivia 28 Dec '05

28 Dec '05

Hello, I have a problem concerning the output_directory in modeller. I changed it on my script but the thing is that it generates errors because the restraint file and the .ini file is not found by the automodel script. Is there a way to only put the models in a file?? instead of modifying the entire output_directory?? Please, help me Olivia --------------------------------- Nouveau : téléphonez moins cher avec Yahoo! Messenger ! Découvez les tarifs exceptionnels pour appeler la France et l'international.Téléchargez la version beta.

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what i am doing wrong?
by Anna Kaczynska 24 Dec '05

24 Dec '05

Dear all, I am just starting with Modeller and I am trying to run the 'basic-example' that is posted on-line, but it does not work. Can you let me know what I am doing wrong? Thank you sincerely Anna Kaczynska Type 'mod8v1 model-default.py' to run Modeller on the script 'model- default.py'. C:\Program Files\Modeller8v1>mod8v1 model-default.py FATAL ERROR: Cannot open file model-default.py: No such file or directory C:\Program Files\Modeller8v1>basic example dir 'basic' is not recognized as an internal or external command, operable program or batch file. C:\Program Files\Modeller8v1>c: C:\Program Files\Modeller8v1>cd basic-example C:\Program Files\Modeller8v1\basic-example>dir Volume in drive C has no label. Volume Serial Number is D0E7-521C Directory of C:\Program Files\Modeller8v1\basic-example 12/23/2005 09:16 PM <DIR> . 12/23/2005 09:16 PM <DIR> .. 12/23/2005 09:10 PM <DIR> basic-example 12/23/2005 09:16 PM 0 dir 1 File(s) 0 bytes 3 Dir(s) 1,568,976,896 bytes free C:\Program Files\Modeller8v1\basic-example>dir Volume in drive C has no label. Volume Serial Number is D0E7-521C Directory of C:\Program Files\Modeller8v1\basic-example 12/23/2005 09:16 PM <DIR> . 12/23/2005 09:16 PM <DIR> .. 12/23/2005 09:10 PM <DIR> basic-example 12/23/2005 09:16 PM 0 dir 1 File(s) 0 bytes 3 Dir(s) 1,568,976,896 bytes free C:\Program Files\Modeller8v1\basic-example>P1;TvLDH 'P1' is not recognized as an internal or external command, operable program or batch file. C:\Program Files\Modeller8v1\basic-example>DIR Volume in drive C has no label. Volume Serial Number is D0E7-521C Directory of C:\Program Files\Modeller8v1\basic-example 12/23/2005 09:16 PM <DIR> . 12/23/2005 09:16 PM <DIR> .. 12/23/2005 09:10 PM <DIR> basic-example 12/23/2005 09:16 PM 0 dir 1 File(s) 0 bytes 3 Dir(s) 1,569,390,592 bytes free C:\Program Files\Modeller8v1\basic-example>P1;TvLDH 'P1' is not recognized as an internal or external command, operable program or batch file. C:\Program Files\Modeller8v1\basic-example>

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modelling loops with nmr restraints
by cubellis＠unina.it 16 Dec '05

16 Dec '05

dear sir , I am trying to model a protein using an alignment to a pdb template and nmr data for a loop which is missing in the pdb template. the input top file that used is the following: INCLUDE SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ATOM_FILES_DIRECTORY = './' SET PDB_EXT = '.pdb' #SET MD_LEVEL = 'refine1' SET HYDROGEN_IO = on #SET DEVIATION = 4.0 SET ALIGNMENT_FORMAT = 'PIR' SET STARTING_MODEL = 1 SET ENDING_MODEL = 10 SET SEQUENCE = 'mysequence' SET ALNFILE = 'my.ali' SET KNOWNS='mytemplatestructure' SET TOPOLOGY_MODEL = 1 SET TOPLIB = '/software/modeller7v7/modlib/top_allh.lib' SET PARLIB = '/software/modeller7v7/modlib/par.lib' CALL ROUTINE = 'model' SUBROUTINE ROUTINE = 'rd_restraints' READ_RESTRAINTS FILE = CSRFILE # This is an additional user provided file: READ_RESTRAINTS FILE = 'nmr.rsr' RETURN END_SUBROUTINE I obtained 10 models but I can see that none of them satisfies all the nmr restraints. therefore I thought to model more thoroughly only the loop for which I have the nmr restraints. could you suggest me how to include in the proper way when I call the loop routine? shall I use again SUBROUTINE ROUTINE = 'rd_restraints' READ_RESTRAINTS FILE = CSRFILE # This is an additional user provided file: READ_RESTRAINTS FILE = 'nmr.rsr' RETURN END_SUBROUTINE ? or shoud I read only the nmr.rsr? or other options? -many thanks mvcubellis ---------------------------------------------------------------- This message was sent using IMP, the Internet Messaging Program.

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DOPE Score
by Mattias de Hollander 16 Dec '05

16 Dec '05

Hi, I've a question about the DOPE score and the profile plot you can make of it using GNUPLOT. I made such a plot with the files from the basic tutorial. When i do the same for my own data, i don't get a nice plot. I made the profiles using the script of the tutorial and the pdb files of my model and template. The data range of the dope score for each residue is different for my model and the template. So you see the line of the template with the line of the model far below it in a straight line (due to the differences in data range) The final DOPE scores are also different. Does this mean i have a wrong model? The model i use is the best of 20 generated models and i did check it with procheck and errat. The last one even gives a good score (84) and doesn't shows any black areas. So, what's wrong? Does the dope score not work on my files? Thanks, Mattias -- Student Bio-Informatics Hogeschool Leiden The Netherlands

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Loop model selection
by bmbbl＠leeds.ac.uk 15 Dec '05

15 Dec '05

Dear Modellers, I have used MODELLER to create 100 11-residue long loop models. Some of models cannot form proper loops, so I used their objective function value as cut-off to select loop models. However further biological structure-function studies of the selected models are not all consistent with the experiment results in vitro. Presumbaly, therefore, some of loop models shouldnot have been selected. Meanwhile I threw the crystal structure of the template into MODELLER to model the loop region, which is the corresponding position in the target model. The loop redefinement of the crystal structure show very similar conformations distribution to the model protein. In the crystal structure, 3 H-bonds stabilise the loop conformation. They are E-R , E-S. However R and S are replaced by P and T in the model sequence. So my questions is what the proper criteria is for this case? Should the conservation of the H-bonds be checked in the loop models? If it is a way how to check H-bonds in 100 loop models automatically before I have some ideas to write a piece of program myself? Many thanks for hints. Binbin

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