I have not tried the same using Modeller 6.1, since the release of Modeller 6.2 is imminent, I thought it would be best to wait and directly install the latest version. I just wanted to know if there seems to be a visible error on my part with the input files etc. Bearing in mind I never got an error message using a single template, I don't understand why this should happen. Do you think this problem could be linked to the fact that I am using Modeller 4?
Any feedback would be appreciated.
Regards, Dinesh PhD student- University of Edinburgh
----Original Message Follows----
From: Bozidar Yerkovich <>
Reply-To:
To: "Dinesh Soares" <>
CC:
Subject: Re: Modeller 4
Date: Mon, 13 May 2002 12:43:52 -0400
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
>
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