Hi,
I am currently using Modeller 4 to try and model a protein of interest. I was able to model this protein "DAF_2" using a single template "MCP_1" while providing the alignment directly for modelling.
However, when I introduce a second template "VCP_1" in the direct alignment, I get the following message (several thousand lines of it!) before the program exits:
chkder___W> DVZ(i) out of bounds: 503 503nan chkder___W> DVX(i) out of bounds: 504 504 0.7392E+14 chkder___W> DVY(i) out of bounds: 504 504 -0.5166E+13 chkder___W> DVZ(i) out of bounds: 504 504 0.3008E+14 chkder___W> DVX(i) out of bounds: 505 505nan chkder___W> DVY(i) out of bounds: 505 505nan chkder___W> DVZ(i) out of bounds: 505 505nan chkder___W> DVX(i) out of bounds: 506 506nan chkder___W> DVY(i) out of bounds: 506 506nan chkder___W> DVZ(i) out of bounds: 506 506nan chkder___W> DVX(i) out of bounds: 507 507nan chkder___W> DVY(i) out of bounds: 507 507nan chkder___W> DVZ(i) out of bounds: 507 507nan getcells__E> internal error; nx,ny,nz,cell,icel,maxcell: ************************ 4.000******** 208000
MY TOP FILE: model-double.top
INCLUDE #include modeller routines SET ALNFILE = 'DAF_2-MCP_1-VCP_3.ali' #alignment file SET KNOWNS = 'MCP_1' 'VCP_3' #known templates SET SEQUENCE = 'DAF_2' #target sequence file SET STARTING_MODEL = 1 SET ENDING_MODEL = 5 #generate 5 models CALL ROUTINE = 'model' #get models
MY ALIGNMENT FILE: DAF_2-MCP_1-VCP_3.ali
>P1;MCP_1 structureX:MCP_1:1:A:61:A:::: -CEEPP-TFEAMELIGKPKP-YYEIGERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACY* >P1;VCP_3 structureX:VCP_3:128:A:183:A:::: KCQSPPSISNGRHNG-Y-ED-FYTDGSVVTYSCNSGYSLI-GNSGVL-CSGG-EWSDP--PTCQ* >P1;DAF_2 sequence:DAF_2 SCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWS-TAVEFCK*
Please advise!! If you require the PDB files, please let me know.
Thanks in advance, Dinesh
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Hi,
Did you try MODELLER 6v1? Do you get the same error with it?
Thanks, Bozidar
On Monday May 13 2002 10:28 am, Dinesh Soares wrote: > Hi, > > I am currently using Modeller 4 to try and model a protein of interest. I > was able to model this protein "DAF_2" using a single template "MCP_1" > while providing the alignment directly for modelling. > > However, when I introduce a second template "VCP_1" in the direct > alignment, I get the following message (several thousand lines of it!) > before the program exits: > > chkder___W> DVZ(i) out of bounds: 503 503nan > chkder___W> DVX(i) out of bounds: 504 504 0.7392E+14 > chkder___W> DVY(i) out of bounds: 504 504 -0.5166E+13 > chkder___W> DVZ(i) out of bounds: 504 504 0.3008E+14 > chkder___W> DVX(i) out of bounds: 505 505nan > chkder___W> DVY(i) out of bounds: 505 505nan > chkder___W> DVZ(i) out of bounds: 505 505nan > chkder___W> DVX(i) out of bounds: 506 506nan > chkder___W> DVY(i) out of bounds: 506 506nan > chkder___W> DVZ(i) out of bounds: 506 506nan > chkder___W> DVX(i) out of bounds: 507 507nan > chkder___W> DVY(i) out of bounds: 507 507nan > chkder___W> DVZ(i) out of bounds: 507 507nan > getcells__E> internal error; nx,ny,nz,cell,icel,maxcell: > ************************ 4.000******** 208000 > > > MY TOP FILE: model-double.top > > INCLUDE #include modeller routines > SET ALNFILE = 'DAF_2-MCP_1-VCP_3.ali' #alignment file > SET KNOWNS = 'MCP_1' 'VCP_3' #known templates > SET SEQUENCE = 'DAF_2' #target sequence file > SET STARTING_MODEL = 1 > SET ENDING_MODEL = 5 #generate 5 models > CALL ROUTINE = 'model' #get models > > > MY ALIGNMENT FILE: DAF_2-MCP_1-VCP_3.ali > > >P1;MCP_1 > > structureX:MCP_1:1:A:61:A:::: > -CEEPP-TFEAMELIGKPKP-YYEIGERVDYKCKKGYFYIPPLATHTICDRNHTWLPVSDDACY* > > >P1;VCP_3 > > structureX:VCP_3:128:A:183:A:::: > KCQSPPSISNGRHNG-Y-ED-FYTDGSVVTYSCNSGYSLI-GNSGVL-CSGG-EWSDP--PTCQ* > > >P1;DAF_2 > > sequence:DAF_2 > SCEVPTRLNSASLKQPYITQNYFPVGTVVEYECRPGYRREPSLSPKLTCLQNLKWS-TAVEFCK* > > > Please advise!! If you require the PDB files, please let me know. > > Thanks in advance, > Dinesh > > _________________________________________________________________ > MSN Photos is the easiest way to share and print your photos: > http://photos.msn.com/support/worldwide.aspx
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Bozidar Yerkovich -
Dinesh Soares