Also I've tried to install Amber tools on another debian machine
there are no problems with X but during compilation I have problems with
RISM program
make[1]: Entering directory `/home/own/amber11/AmberTools/src/rism'
cpp -traditional -P -DBINTRAJ -DRISM -DRISM_CRDINTERP -DRISM_DX
-DRISM_LINPROJ safemem.f > _safemem.f
gfortran -c -O3 -mtune=generic -msse -mfpmath=sse -ffree-form -o
safemem.o _safemem.f
_safemem.f:105.40:
type(memTracker),private :: totalMem
1
Error: Object 'totalmem' at (1) must have the SAVE attribute for default
initialization of a component
make[1]: *** [safemem.o] Error 1
make[1]: Leaving directory `/home/own/amber11/AmberTools/src/rism'
make: *** [serial] Error 2
What should I do?
2011/10/31 James Starlight <jmsstarlight.gmail.com>
> 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
>>>
>>
>>
>
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Received on Tue Nov 01 2011 - 00:30:03 PDT
