AMBER Archive (2005)

Subject: RE: AMBER: sander prob

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sat Sep 17 2005 - 11:23:27 CDT

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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel: +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of cbala_at_igib.res.in
> Sent: Saturday, September 17, 2005 03:29
> To: amber_at_scripps.edu
> Subject: Re: AMBER: sander prob
>
>
> Sir,
>
> I could found that it was an installation error. i hve pasted
> the error i
> got during i run the "make serial" and "make test" option. i hve
> gone through the mail archieve also but i couldnt get what i should do
> exactly to solve this. except sander other programs are working.
>
> when i do make serial, i get the following,
> --------------------------------------------------------------
> ---------------
> Starting installation of Amber8 (serial) at Sat Sep 17
> 14:47:46 IST 2005.
> mkdir ../exe
> mkdir: cannot create directory `../exe': File exists
> make: [serial] Error 1 (ignored)
> cd lib; make install
> make[1]: Entering directory `/usr/local/amber8/src/lib'
> cpp -traditional -P -I/usr/local/amber8/src/include new2oldparm.f >
> _new2oldparm.f
> ifort -c -w95 -tpp7 -mp1 -O0 -o new2oldparm.o _new2oldparm.f
> make[1]: ifort: Command not found
> make[1]: *** [new2oldparm.o] Error 127
> make[1]: Leaving directory `/usr/local/amber8/src/lib'
> make: *** [serial] Error 2
> --------------------------------------------------------------
> ---------------
>
> when i do make test, following error comes
> --------------------------------------------------------------
> ---------------
>
> cd dmp; /Run.dmp
> ../../exe/sander: Command not found.
> ./Run.dmp: Program error
> make: *** [test.sander.no_lmod] Error 1
> --------------------------------------------------------------
> ---------------
>
> Kindly help me,
> Thanks,
> Bala
>
>
> On 9/16/2005, "Carlos Simmerling" <carlos_at_ilion.bio.sunysb.edu> wrote:
>
> >it sounds like your path isn't set right. there are lots of
> >ways to resolve that, it depends on how much Unix
> >you know. the simplest might be to put the entire path
> >for sander in the script.
> >
> >cbala_at_igib.res.in wrote:
> >
> >>dear users,
> >>
> >>i hve installed ifc90 and amber8 in an intel p4 machine
> with fedora core
> >>4. when i export the path and run xleap, its working fine
> but when i run
> >>sander (for mininimisation), it shows the message "bash
> sander: command
> >>not found".
> >>
> >>kindly suggest me a solution.
> >>thanks in advance,
> >>Bala
> >>------------------------------------------------------------
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> >>
> >
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