Jason, hello
I'm using latest Debian mint
I've found those files
own src # 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
How I can modify configure script to include that files in it ? I'm not
enought good in linux yet :)
James
2011/10/31 Jason Swails <jason.swails.gmail.com>
> 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
> _______________________________________________
> 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
Received on Mon Oct 31 2011 - 07:30:03 PDT
