May 2004 - modeller_usage

objective function
by Gianluca Croce 17 May '04

17 May '04

Hi all, I'm a new user of modeller and I would like to know which it is the measure unit used from mod6v2 for the objective function? It is possible to have a correlation between the unit of objective function and other units (Kcal/mol, KJ/mol etc)? Regards, G. -- Gianluca Croce Ph. D. Student DISTA- Universita' del Piemonte Orientale C.so T. Borsalino 54, Alessandria I-15100 Italy Tel_office: +39 0131 287414 Fax: +39 0131 287416 visit my Web page at the URL: www.mfn.unipmn.it/~gcroce

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different results running mod6v2 on diff OS
by nurul bahiyah 17 May '04

17 May '04

hi all, i tried to run modeller both on SGI IRIX and windows platform and i got different results for both. is this normal? shouldnt it be producing structures with identical coordinates no matter what OS being used? thanks all

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toppar files for Charmm and X-plor
by Han Choe 16 May '04

16 May '04

Dear Modellers, Topology and parameter files for compounds are relatively easy to find for X-plor format rather than for Charmm format that is used for the Modeller program in the websites. What are the major differences of the files between X-plor format and Charmm format? Is there an easy way to convert the X-plor format to the Charmm format? Cheers, Han

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alignment file!
by Yue Yun 07 May '04

07 May '04

Hello everyone, I got the following error message when Modeller reads my alignment file: rdpir___270E> Error reading/processing file: my.ali recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Here's my input file: >P1;1Q4G structureX:1Q4G:32:A:584:A:::: PVNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHF LLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRI LPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFK TSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPV LMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQT ARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLM PDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDV IKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEK CHPNSIFGESMIEMGAPFSLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLN TKTCPYVSFHVPD* >P1;1EBV sequence -VNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHF LLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRI LPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFK TSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPV LMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQT ARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLM PDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDV IKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEK CHPNSIFGESMIEMGAPFXLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLN TKTCPYVSFHVP-* Here's my .top file: # Homology modelling by the MODELLER TOP routine 'model'. INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'my.ali' # alignment filename SET KNOWNS = '1Q4G' # codes of the templates SET SEQUENCE = '1EBV' # code of the target SET ATOM_FILES_DIRECTORY = './:../atom_files' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling Can anyone help me to solve this question? I download the 1Q4G.pdb file from the www.pdb.org. Thank you!

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Help!!
by Chaitanya Reddy.A 07 May '04

07 May '04

Dear all, We are modelling a molecule but we are facing a problem to which i am unable to find it. We hope you can help me in this regard. We want to model a map kinase 8 using the map kinase 10 molecule which shows 93% homology. We aligned using clustalx and we submitted to modeller as .ali file. Below is the alignment file we obtained from clustalx >P1;1jnk structureX:1jnk:1 : :346 : :C-JUN N-TERMINAL KINASE::-1.00: 2.30 ------DNQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELV LMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHR DLKPSNIVVKSDCTLKILDFGLA-----SFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILF PGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSK MLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPP-----QLDEREHTIEEWKELIYKEVMN------------- ----------------------------------------------------* >P1;output sequence:output:1 : :427 : :JNK mitogen-activated protein kinase:2.40:-1.00:-1.00 MSRSKRDNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIKKLSRPFQNQTHAKRAYRELV LMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHR DLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDLWSVGCIMGEMVCHKILF PGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSK MLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYKEVMDLEERTKNGVIRGQ PSPLGAAVINGSQHPSSSSSVNDVSSMSTDPTLASDTDSSLEAAAGPLGCCR* After submitting to modeller, the following is the error.. The error message rdabrk__288W> Protein not accepted: 1 rdabrk__290E> Number of residues in the alignment and pdb files are different: 346 0 For alignment entry: 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Please help me in solving this problem. But we manually examined the number of residues in both pdb files and alignment files and we found no difference. Regards Chaitu

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Fwd: homology-based secondary structure modelling
by Amanda Preston 05 May '04

05 May '04

could you please post the attached inquiry on the MODELLER forum? thanks, amanda --- Amanda Preston <amandaraepreston(a)yahoo.com> wrote: > From Amanda Preston Sun Apr 25 19:09:23 2004 > Received: from [4.224.45.52] by web21208.mail.yahoo.com via HTTP; Sun, 25 Apr 2004 19:09:23 PDT > Date: Sun, 25 Apr 2004 19:09:23 -0700 (PDT) > From: Amanda Preston <amandaraepreston(a)yahoo.com> > Subject: homology-based secondary structure modelling > To: sali(a)salilab.org > MIME-Version: 1.0 > Content-Type: text/plain; charset=us-ascii > Content-Length: 446 > > > > i was hoping someone might be able to give me some general information. i'm rather new to > this > > field and i'm having trouble finding resources to obtain computer programs/software for > > homology-based secondary structure modelling. can you give me some advice on where i can > obtain > > such software? in specific, i'm hoping to be able to find a program that can model a rpotein > whose primary structure is unknown. > > > > thanks, > > amanda > > > >

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loop refinement
by Karsten Suhre 05 May '04

05 May '04

Dear Modeller users, I am looking for a simple MODELLER top-script that allows to remodel an already existing loop of a protein while leaving the rest of the molecule unchanged, that is, the input would be a single PDB file and a residue range. The idea is to generate a number of different conformations of that loop and to evaluate them against X-ray crystallographic data (I am trying to model a loop that is only barely visible in a low resolution dataset). Thank you very much in advance, Kind regards, Karsten Suhre, IGS-CNRS, Marseille, France.

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modeller6v2 on apple macitosh G5 machine.
by Wonsuhk Uhm 04 May '04

04 May '04

Hi all. I am trying to use modeller6v2 on my Apple G5 Mac with MacOS 10.3.3 (panther). But whenever I was running modeller, it gave segmentation fault error as follows; /Users/wsum/Desktop/Projects/modeller6v2/bin/mod6v2: line 39: 4504 Segmentation fault ${EXECUTABLE} ${STEERF} >${LOGF} Dose anyone know of the solution for this error ? Thanks in advance Wonsuhk Uhm, PhD.

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help on using modeller
by rathan kar 03 May '04

03 May '04

hi all iam a fresher working on modeller and nothing is going on here properly . i use a win me machine with mod6v2 installed. i tried an alignment file to model but its not working .i have included the top files for reference INCLUDE # Include the predefined TOP routines SET OUTPUT_CONTROL = 1 1 1 1 1 # uncomment to produce a large log file SET ALNFILE = 'alignmentfile.ali' # alignment filename SET KNOWNS = '1HM9' # codes of the templates SET SEQUENCE = 'query' # code of the target SET ATOM_FILES_DIRECTORY = 'c:/mod6v2/bin/1hm9.pdb' # directories for input atom files SET STARTING_MODEL= 1 # index of the first model SET ENDING_MODEL = 1 # index of the last model # (determines how many models to calculate) CALL ROUTINE = 'model' # do homology modelling i dont know what does this atom_files mean.plz explain the ERROR it shows is as follows: openf5___224_>open 11 OLD SEQUENTIAL alignmentfile.ali rdpir___376W>not enough fields in the sequence line of the sequence entry:sequence:query:1::165 : : actual fields should be: 7 10 (Fields are separated by a colon. :) read_al_375E>unknown residue type,Position , Sequence: 1 1 recover_____E>ERROR_STATUS=>STOP_ON_ERROR 1 1 Yahoo! India Matrimony: Find your partner online.

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Re: modeller_usage Digest, Vol 3, Issue 51
by rathan kar 03 May '04

03 May '04

hi this is the error file nce:query:1 : :165: :unknown Actual fields, should be: 7 10 (Fields are separated by a colon, :) Dynamically allocated memory at amaxbnd [B,kB,MB]: 4967329 4850. 907 4.737 openf5__224_> Open 11 OLD SEQUENTIAL alignmentfile.ali rdpir___376W> Not enough fields in the second line of the sequence entry: seque nce:query:1 : :165: :unknown Actual fields, should be: 7 10 (Fields are separated by a colon, :) read_al_375E> Unknown residue type,position,sequence: 1 1 recover____E> ERROR_STATUS >= STOP_ON_ERROR: 1 1 Dynamically allocated memory at finish [B,kB,MB]: 4967329 4850. 907 4.737 Starting time : 2004/05/03 18:32:30. 510 Closing time : 2004/05/03 18:32:37. 150 Total CPU time [seconds] : 6.97 C:\mod6v2\bin> C:\mod6v2\bin> and the alignment file is >P1;1hm9 structureX:1hm9:2 : :183: :glmu SNFAIILAAGKGTRMKSDLPKVLHKVAGISMLEHVFRSVGAIQPEKTVTVVGHKAELVEEVLAGQTE -FVTQSEQLGTG-HAVMMTEPILEGLSGHTLVIAGDTPLITGESLKNLIDFHINHKNVATILTAETD NPF-GYGRIVRND--NAEVLRIVEQKDATDFEKQIKEINTGT-YVFDNERLFEA* >P1;query sequence:query:1 : :165: :unknown SLKVIILAGGRGKRIT--LFKPFLVVCGKPLISWAFDAVNKL-SDKVYTVVGHKAELVEEVLAGQTE IFPTPDISYENDVKYVV------ESLGPPILVLPVDIAFINNNIINNLIERCA--------VDMCTL KSYGSYLGVTYWTGLNFSNYTDIEVK-----EKL-YNINTWEDYIKANKECNIL* plz reply Yahoo! India Matrimony: Find your partner online.

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