Hi Syed,
I think you are seeing the same problem that is mentioned in some of the
links to the amber mailing list archive. I don't think we have ever been
able to locate what causes this problem however...
One option would be to try changing the c compiler. If you have the Intel
compilers installed (ifort / icc) then try, assuming you have an x86_64
machine and the 64 bit version of the compilers (fce/cce) and OS installed:
./configure -static -nopar ifort_x86_64
Then edit config.h and change gcc to icc and g++ to icpc.
Then make clean, make
See if xleap then works in this situation.
All the best
Ross
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> -----Original Message-----
> From: owner-amber.scripps.edu
> [mailto:owner-amber.scripps.edu] On Behalf Of Syed Tarique Moin
> Sent: Tuesday, June 12, 2007 01:05
> To: amber.scripps.edu
> Subject: Re: AMBER: problem in installing amber9
>
> Hi
>
> Thanks for you kind suggestion,
>
> But i want to update with amber9, so plz guide me for
> the installation,
>
> I have compiler g98 and the Hardware is Intel Xeon
> dual processor.
>
> Regard
> --- "David A. Case" <case.scripps.edu> wrote:
>
> > On Fri, Jun 01, 2007, Syed Tarique Moin wrote:
> >
> > > I installed amber9 but not looking fine, i have a
> > > problem in xleap, that when i make initial files,
> > like
> > > using the command
> > >
> > > solvatebox or addions the solvent surrounding the
> > > solute not well file (file attached name as
> > > amber9.jpg)
> > >
> > > but its looking right with amber7.jpg (for the
> > > comparison) surrounding the solute very well by
> > the
> > > solvent.
> > >
> >
> > Please see if this helps:
> >
> >
> > http://amber.ch.ic.ac.uk/archive/200406/0298.html
> >
> > or this:
> >
> > http://amber.ch.ic.ac.uk/archive/200503/0122.html
> >
> > or this:
> >
> > http://amber.ch.ic.ac.uk/archive/200610/0205.html
> >
> > Since Amber 7 works, you can still use that, I would
> > imagine. You might
> > provide details about your compiler and what
> > architecture (emt64?) you are
> > using.
> >
> > ....dac
> >
> >
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>
>
> Syed Tarique Moin,
> Junior Research Fellow,
> H.E.J. Research Institute of Chemistry,
> International Center for Chemical and Biological Sciences,
> University of Karachi, Karachi-75720, Pakistan
>
> tarisyed.yahoo.com
> tarisyed.hotmail.com
>
>
>
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Received on Wed Jun 13 2007 - 06:07:39 PDT
