- modeller_usage - salilab.org

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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secondary structure display
by gowthaman ramasamy 30 Apr '04

30 Apr '04

hello list, This is not a Modeller related question, so bear with me. But I wonder if some one knows about this. I would like to display the secondary structure of a protein models graphically along with their sequence (as seen in RCSB's pdb summary page). does any one know of some stand alone software which does it. many thanks in advance gowtham -- Ra. Gowthaman, Graduate Student, Bioinformatics Lab, Malaria Research Group, ICGEB , New Delhi. INDIA Phone: 91-9811261804 91-11-26173184; 91-11-26189360 #extn 314

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READ_MODEL error: MODEL atom not classified
by Sascha Tayefeh 28 Apr '04

28 Apr '04

Dear community, I am trying to get warm with modeller-usage by checking out the official manual's examples. For some reason, the READ_MODEL command does not work. Here's my input/output: *************** INPUT ************************** READ_TOPOLOGY FILE = '/soft/modeller6v2/modlib/top.lib', TOPOLOGY_MODEL = 3 READ_PARAMETERS FILE = '/soft/modeller6v2/modlib/par.lib' READ_MODEL FILE = '1P7B' *************** OUTPUT ************************** iatmcls_286W> MODEL atom not classified: VAL:OT1 VAL iatmcls_286W> MODEL atom not classified: VAL:OT1 VAL Using different pdbs (eg. manual's suggested 1fas), I get the same error with different residues. *************** OUTPUT ************************** iatmcls_286W> MODEL atom not classified: TYR:OT1 TYR iatmcls_286W> MODEL atom not classified: TYR:OT2 TYR I have checked the pdbs for OT1 - there is simply no such entry, so: what's the problem? Also, I have tried modeller on different platforms (linux, irix etc). Thanx for any help in advance S. Tayefeh (Grad. Stud.) Technical University Darmstadt Dept. of Phys. Chemistry Germany

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