I solved my problems just unlocking the Numlock!! I found it in other
threads on this mailiniglist.
However, I tried the make test.sander to verify my installation of
amber7...but it really tekes a long time (hours) in the last step
[Rossella.topolone test]$ make test.sander
cd dmp; ./Run.dmp
diffing mdout.dmp.save with mdout
PASSED
==============================================================
cd adenine; ./Run.adenine
diffing mdout.adenine.save with mdout
PASSED
==============================================================
cd cytosine; ./Run.cytosine
diffing cytosine.out.save with cytosine.out
PASSED
==============================================================
cd nonper; ./Run.nonper
diffing mdout.nonper.save with mdout.nonper
PASSED
==============================================================
cd nonper; ./Run.nonper.belly
diffing mdout.belly.save with mdout.belly
PASSED
==============================================================
cd nonper; ./Run.nonper.min
diffing mdout.min.save with mdout.min
PASSED
==============================================================
cd nonper; ./Run.cap
diffing mdout.cap.save with mdout.cap
PASSED
==============================================================
cd nonper; ./Run.nonper.nocut
diffing mdout.nocut.save with mdout.nocut
PASSED
==============================================================
cd tip4p; ./Run.tip4p
diffing mdout.tip4p.save with mdout
PASSED
==============================================================
cd tip5p; ./Run.tip5p
diffing mdout.tip5p.save with mdout
PASSED
==============================================================
cd 4096wat; ./Run.pure_wat
diffing mdout.pure_wat.save with mdout
PASSED
==============================================================
cd dhfr; ./Run.dhfr
diffing mdout.dhfr.save with mdout
PASSED
==============================================================
cd gb_rna; ./Run.gbrna
diffing mdout.gbrna.save with mdout
PASSED
==============================================================
cd gb_rna; ./Run.gbrna.min
diffing mdout.gbrna.min.save with mdout.min
PASSED
==============================================================
cd gbsa_xfin; ./Run.gbsa
diffing mdout.gbsa.save with mdout
PASSED
==============================================================
cd polarizable_water; ./Run.pol_wat
diffing mdout.polwat.save with mdout
PASSED
==============================================================
cd ubiquitin; ./Run.ubiquitin
diffing mdout.ubiquitin.save with mdout
PASSED
==============================================================
cd dna_pol; ./Run.dna_pol
diffing mdout.dna_pol.save with mdout
PASSED
==============================================================
cd aspash; ./Run.aspash
diffing mdout.aspash.save with mdout
PASSED
==============================================================
cd ion_wat; ./Run.ion_wat
diffing mdout.ion_wat.save with mdout
PASSED
==============================================================
cd circ_dna; ./Run.circdna
diffing mdout.circdna.save with mdout
PASSED
==============================================================
cd gb2_trx; ./Run.trxox
diffing mdout.trxox.save with mdout
PASSED
==============================================================
cd tgtmd/change_target; ./Run.tgtmd
SANDER: Targeted MD with changing target
This step seemed to be too long and i stopped.. what do you think?
Thanks.
2010/9/20 Jason Swails <jason.swails.gmail.com>
> Hello,
>
> There are a number of problems with xleap that old that wasn't uncovered
> until 64-bit OSes became the standard. I would suggest that you download
> AmberTools-1.4 which is released under an open source license and is free
> of
> charge. If you still cannot update a free package, then you will probably
> have numerous unsolved and difficult-to-solve bugs with tleap and xleap.
>
> Good luck!
> Jason
>
> On Mon, Sep 20, 2010 at 6:13 AM, Rossella Noschese <
> noschese.rossella.gmail.com> wrote:
>
> > sorry, the scroll menu (file, edit, verbosity)..!!
> >
> > 2010/9/20 Rossella Noschese <noschese.rossella.gmail.com>
> >
> > > Hi, I've just installed amber7 (the only licensed software we have at
> > > work...no possibility to upgrade) on Fedora 13.
> > > I tried running xleap and this is the error in the shell:
> > > [Rossella.topolone ~]$ xleap
> > > -I: Adding /home/Rossella/amber7/dat/leap/prep to search path.
> > > -I: Adding /home/Rossella/amber7/dat/leap/lib to search path.
> > > -I: Adding /home/Rossella/amber7/dat/leap/parm to search path.
> > > -I: Adding /home/Rossella/amber7/dat/leap/cmd to search path.
> > > Warning: Cannot convert string
> > "-*-helvetica-medium-r-*-*-18-*-*-*-*-*-*-*"
> > > to type FontStruct
> > > Warning: Cannot convert string "-*-helvetica-bold-r-*-14-*" to type
> > > FontStruct
> > > Warning: Cannot convert string
> > "-*-helvetica-medium-o-*-*-14-*-*-*-*-*-*-*"
> > > to type FontStruct
> > > Warning: Cannot convert string "-*-courier-bold-r-*-*-14-*-*-*-*-*-*-*"
> > to
> > > type FontStruct
> > > Warning: Cannot convert string
> > "-*-helvetica-medium-o-*-*-18-*-*-*-*-*-*-*"
> > > to type FontStruct
> > > Warning: Cannot convert string "*-*-medium-r-*-14-*-m-*" to type
> > FontStruct
> > > the scroll bar doesn't work
> > > I've already the xorg-x11-fonts-misc package installed... so do you
> have
> > > an idea of what's the problem?
> > > thanks
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Sep 21 2010 - 01:30:05 PDT
