Hi Bozidar,

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: bozidar@salilab.org

To: "Dinesh Soares"

CC: modeller_usage@salilab.org

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

> _________________________________________________________________

> MSN Photos is the easiest way to share and print your photos:

> http://photos.msn.com/support/worldwide.aspx