-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali@salilab.org; Web http://salilab.org

-----Original Message----- From: Andrej Sali [mailto:sali@salilab.org] Sent: Wednesday, March 05, 2003 7:05 PM To: 'Urmi Doshi' Subject: RE: New to Modeller !!

I suggest you run the executable directly

$MODINSTALL6v2/bin/mod6v2_iris4d modfile.top

Check that the executable is identified as such (the x flag in the ls -ls output), and make sure it did not get corruputed during ftp.

If you cannot set the stacksize limit to a large enough value, you need to ask your sysadmin to do it for you. Some sysadmins set system wide limitations that are frequently not very helpful ;-) I am not sure this is the problem here ...

Andrej

-- Andrej Sali, Professor Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, and California Institute for Quantitative Biomedical Research Mission Bay Genentech Hall 600 16th Street, Suite N472D University of California, San Francisco San Francisco, CA 94143-2240 (CA 94107 for direct delivery by courier) Tel +1 (415) 514-4227; Fax +1 (415) 514-4231 Tel Assistant +1 (415)514-4228; Lab +1 (415) 514-4232, 4233, 4239 Email sali@salilab.org; Web http://salilab.org

> -----Original Message----- > From: owner-modeller_usage@salilab.org > [mailto:owner-modeller_usage@salilab.org] On Behalf Of Urmi Doshi > Sent: Wednesday, October 02, 2002 3:30 PM > To: modeller_usage@salilab.org > Subject: Re: New to Modeller !! > > > Thank you all. I tried mod and mod6v2 , but doesn't run. I > get this message everytime I start the UNIX shell limit > stacksize unlimited : can't remove limit which is set in > .cshrc. Is this the reason why modeller does not seem to work? -Urmi > ----- Original Message ----- > From: "Peter C. Lai" sirmoo@cowbert.2y.net > To: "Luis Rosales" ludwig@biomedicas.unam.mx > Cc: "Bozidar Yerkovich" bozidar@salilab.org; "Urmi Doshi" > urdoshi@wam.umd.edu; modeller_usage@salilab.org > Sent: Tuesday, March 04, 2003 7:51 PM > Subject: Re: New to Modeller !! > > > > I am using a default installation on my SGI Octane. 'mod6v2' is the > > shell script in $MODINSTALL6v2/bin, which calls mod6v2_iris4d (since > > iris4d is what > $EXECUTABLE_TYPE6v2 is > > set > to) > > LIBS_LIB6v2 is set to $MODINSTALL6v2/modlib/libs.lib. > > > > hope that helps in terms of configuration. > > > > On Tue, Mar 04, 2003 at 04:53:01PM -0600, Luis Rosales wrote: > > > Hi: > > > > > > Maybe your command for modeller is not "mod", mine is > mod6v2 and is > > > the default I got from the installation script... > > > > > > Hope this helps, > > > > > > Luis > > > > > > > > > ----- Original Message ----- > > > From: "Bozidar Yerkovich" bozidar@salilab.org > > > To: "Urmi Doshi" urdoshi@wam.umd.edu > > > Cc: modeller_usage@salilab.org > > > Sent: Tuesday, March 04, 2003 3:36 PM > > > Subject: Re: New to Modeller !! > > > > > > > > > > > > > > Urmi, > > > > Did you source your .cshrc file? > > > > Bozidar > > > > > > > > On Tue, 1 Oct 2002, Urmi Doshi wrote: > > > > > > > > > Hi, > > > > > > > > > > I have just installed Modeller exactly the way as given in the > User's > > > Manual on an SGI Fuel. However, when I try running the > command "mod > > > model-default" which is a script file available with > modeller, the > > > error message I get is " 'mod' command not found". > > > > > > > > > > I am sure there's something silly that I am missing, but can't > figure > > > out. Is there any stack requirement for running MODELLER on SGI > > > FUEl? > > > > > Can anyone help me start using MODELLER ? > > > > > > > > > > - Urmi Doshi > > > > > > > > > > > > > > > -- > > Peter C. Lai > > University of Connecticut > > Dept. of Molecular and Cell Biology > > Yale University School of Medicine > > SenseLab | Research Assistant > > http://cowbert.2y.net/ > > > > >