Which Debian are you using, and which version of that OS are you using? If
your version is new enough, you may have to change the default place where
configure searches for them in the configure script itself.
I think AmberTools 1.5 only looks in /usr/X11R6/lib or /usr/X11R6/lib64,
even though it may need to just look in /usr/lib or /usr/lib64.
If this is the case, try making the above change in the configure script to
see if that works (but first you have to make sure that libXt.so or libXt.a
are present in any of the above directories).
HTH,
Jason
On Mon, Oct 31, 2011 at 9:23 AM, James Starlight <jmsstarlight.gmail.com>wrote:
> Dan, hello!
>
> I've installed xorg-dev by apt-get but my problem have not been solved (
>
> Is there any other required packages?
> May be I must add xorg-dex to path or something else?
>
> Thanks for help,
>
> James
>
> 2011/10/31 Daniel Roe <daniel.r.roe.gmail.com>
>
> > Hi,
> >
> > The xleap part of the configure script is a little confusing and the
> > error message is a little misleading. It's not enough to have the
> > libraries installed, you need the development headers as well; this is
> > implied by the package names but not clearly stated.
> >
> > I believe on debian you need to make sure that the package "xorg-dev"
> > is installed. After that configure should work properly.
> >
> > -Dan
> >
> > On Mon, Oct 31, 2011 at 3:42 AM, James Starlight <jmsstarlight.gmail.com
> >
> > wrote:
> > > I've found why xleap have not been installed by I could not dix this
> > problem
> > >
> > > during configure I've found that
> > >
> > > Could not find the X11 libraries; you may need to edit config.h
> > > to set the XHOME and XLIBS variables.
> > > Warning: the X11 libraries are not in the usual location !
> > > To search for them try the command: locate libXt
> > > On new Fedora OS's install the libXt-devel libXext-devel
> > > libX11-devel libICE-devel libSM-devel packages.
> > > On old Fedora OS's install the xorg-x11-devel package.
> > > On RedHat OS's install the XFree86-devel package.
> > > On Ubuntu OS's install the xorg-dev package.
> > > For the moment Amber will be configured not to build XLEaP.
> > >
> > > I've located my Xlibs
> > > own.own ~/Desktop $ locate libXt
> > > /usr/lib/libXtst.so.6
> > > /usr/lib/libXtst.so.6.1.0
> > > /usr/lib/i386-linux-gnu/libXt.a
> > > /usr/lib/i386-linux-gnu/libXt.so
> > > /usr/lib/i386-linux-gnu/libXt.so.6
> > > /usr/lib/i386-linux-gnu/libXt.so.6.0.0
> > >
> > > and that add them to path by
> > > export XLIBS=/usr/lib/i386-linux-gnu/
> > > export PATH=$XLIBS:$PATH
> > >
> > > but It could not solve that problem
> > >
> > > how I could add this values to the configure script directly?
> > >
> > >
> > >
> > > 2011/10/30 James Starlight <jmsstarlight.gmail.com>
> > >
> > >> Hi, Dan!
> > >>
> > >> Thank you for your responce
> > >>
> > >> but I stil have problems with xleap :)
> > >> I've compiled AmberTools with default options listened in manual but
> > xleap
> > >> have not been installed ( it present only in the scr ). There is only
> > shell
> > >> version tleap.
> > >>
> > >> What should I do to install xleap in the alrady built ambertools?
> > >>
> > >> James
> > >>
> > >> 2011/10/30 Daniel Roe <daniel.r.roe.gmail.com>
> > >>
> > >>> Hi,
> > >>>
> > >>> http://ambermd.org/tutorials/
> > >>>
> > >>> Particularly tutorial B1 should help you get started.
> > >>>
> > >>> On Sun, Oct 30, 2011 at 3:45 AM, James Starlight <
> > jmsstarlight.gmail.com>
> > >>> wrote:
> > >>> > Also It's not quite understand for me how properly run different
> > amber
> > >>> > tools programs.
> > >>> >
> > >>> > E..g from subdirectory /own/Documents/amber11/AmberTools/bin
> > >>> > I can run all programs but from another directory that programs are
> > not
> > >>> > aviable ( I've add the Bin to the path but it didnt work )
> > >>>
> > >>> For AmberTools to work properly you need to both set the environment
> > >>> variable AMBERHOME and add $AMBERHOME/bin to your path. For bash this
> > >>> is:
> > >>>
> > >>> export AMBERHOME=/own/Documents/amber11
> > >>> export PATH=$AMBERHOME/bin:$PATH
> > >>>
> > >>> For tcsh/csh this is:
> > >>>
> > >>> setenv AMBERHOME /own/Documents/amber11
> > >>> setenv PATH $AMBERHOME/bin:$PATH
> > >>>
> > >>> > Finally as I understood LEAP have GUI. How I can run this one ?
> > >>>
> > >>> Use xleap. To view the molecule once you've created/loaded it, use
> the
> > >>> 'edit' command, e.g.:
> > >>>
> > >>> source leaprc.ff10
> > >>> m = loadpdb mypdb.pdb
> > >>> edit m
> > >>>
> > >>> See the AmberTools manual for more details. One note: due to a small
> > >>> bug in xleap make sure NUMLOCK is off in order to properly access the
> > >>> menus. Good luck!
> > >>>
> > >>> -Dan
> > >>>
> > >>>
> > >>> --
> > >>> -------------------------
> > >>> Daniel R. Roe, PhD
> > >>> Postdoctoral Associate
> > >>> BioMaPS Institute, Rutgers University
> > >>> 610 Taylor Road
> > >>> Piscataway, NJ 08854
> > >>>
> > >>> _______________________________________________
> > >>> AMBER mailing list
> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>
> > >>
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > -------------------------
> > Daniel R. Roe, PhD
> > Postdoctoral Associate
> > BioMaPS Institute, Rutgers University
> > 610 Taylor Road
> > Piscataway, NJ 08854
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Mon Oct 31 2011 - 07:00:05 PDT
