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!
You need the same fields for your sequence as your template P1;1EBV sequence:1EBV:starting residue:chain:ending residue:chain:::: > VNPCCYYPCQHQGICVRFGLDRYQCDCTRTGYSGPNCTIPEIWTWLRTTLRPSPSFIHF > LLTHGRWLWDFVNATFIRDTLMRLVLTVRSNLIPSPPTYNIAHDYISWESFSNVSYYTRI > LPSVPRDCPTPMGTKGKKQLPDAEFLSRRFLLRRKFIPDPQGTNLMFAFFAQHFTHQFFK > TSGKMGPGFTKALGHGVDLGHIYGDNLERQYQLRLFKDGKLKYQMLNGEVYPPSVEEAPV > LMHYPRGIPPQSQMAVGQEVFGLLPGLMLYATIWLREHNRVCDLLKAEHPTWGDEQLFQT > ARLILIGETIKIVIEEYVQQLSGYFLQLKFDPELLFGAQFQYRNRIAMEFNQLYHWHPLM > PDSFRVGPQDYSYEQFLFNTSMLVDYGVEALVDAFSRQPAGRIGGGRNIDHHILHVAVDV > IKESRVLRLQPFNEYRKRFGMKPYTSFQELTGEKEMAAELEELYGDIDALEFYPGLLLEK > CHPNSIFGESMIEMGAPFXLKGLLGNPICSPEYWKASTFGGEVGFNLVKTATLKKLVCLN > TKTCPYVSFHVP* > in the file my.ali and erase the '-'s.
On Thursday, May 6, 2004, at 08:27 PM, Yue Yun wrote:
> 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! > > > _______________________________________________ > modeller_usage mailing list > modeller_usage@salilab.org > http://salilab.org/mailman/listinfo/modeller_usage >
participants (2)
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Darren Thompson -
Yue Yun