AMBER Archive (2009)

Subject: Re: [AMBER] amber9 in fedora10

From: Bala subramanian (bala.biophysics_at_gmail.com)
Date: Thu Jul 02 2009 - 03:05:55 CDT

Sir,

I searched in google and i found that libXt-devel has to be installed in
Fedora to get IntrinsicP.h and ShellP.h libraries. I installed the
libXt-devel and i did not get the error i got before but instead the
installation stopped with a new error. It says 'cannot find Xext'. But
searching in /usr/lib, i found the presence of libXext.

ls /usr/lib/libXe*

/usr/lib/libXevie.so.1 /usr/lib/libXevie.so.1.0.0 /usr/lib/libXext.so.6
/usr/lib/libXext.so.6.4.0

gcc -o xaLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o
avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o
vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o
ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o
collection.o container.o internal.o list.o loop.o molecule.o oDouble.o
oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o
graphUtil.o select.o amber.o build.o elements.o library.o chirality.o
minimizer.o model.o parmLib.o pdbFile.o tools.o variables.o parser.o help.o
helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o xTank.o
xAction.o x3d.o xBasics.o xaLeapc.o xaUnitEditor.o xaTable.o xaAtomTable.o
XrawRegistr.o xaCommand.o xaTools.o xaAtomParmTable.o xaBondParmTable.o
xaAngleParmTable.o xaParmEditor.o xaTorsionParmTable.o
xaImproperParmTable.o xaHBondParmTable.o ../Xraw/libXaw.a ../Wc/libWcLeap.a
../Xpm/libXpm.a ../Xmu/libXmu.a -L/usr/X11R6/lib -lXt -lXext -lSM -lICE
-lX11 -lm -lpthread
/usr/bin/ld: cannot find -lXext
collect2: ld returned 1 exit status
make[2]: *** [xaLeap] Error 1
make[2]: Leaving directory `/usr/local/amber9/src/leap/src/leap'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/usr/local/amber9/src/leap'
make: *** [serial] Error 2

On Thu, Jul 2, 2009 at 9:02 AM, Bala subramanian
<bala.biophysics_at_gmail.com>wrote:

> Dear Dr. Ross,
>
> I have attached the full error file. It says IntrinsicP.h and ShellP.h : No
> such file or directory.
> I dnt find these files when i give locate IntrinsicP.h or ShellP.h. Do
> these files belong to X11 devel libraries ?. Should i install some other
> libraries also. Because X11 devel libraries are already installed.
>
> Bala
>
>
> On Wed, Jul 1, 2009 at 6:36 PM, Ross Walker <ross_at_rosswalker.co.uk> wrote:
>
>> Dear Bala,
>>
>> Please post the complete error message, even what you gave in the attached
>> file does not contain the full log. I suspect the actual error is a
>> problem
>> finding the X11 development libraries. Even though you have them
>> installed,
>> being Fedora they are probably in some completely non standard place.
>>
>> All the best
>> Ross
>>
>> > -----Original Message-----
>> > From: amber-bounces_at_ambermd.org [mailto:amber-bounces_at_ambermd.org] On
>> > Behalf Of Bala subramanian
>> > Sent: Wednesday, July 01, 2009 7:09 AM
>> > To: AMBER Mailing List
>> > Subject: [AMBER] amber9 in fedora10
>> >
>> > Friends,
>> >
>> > I was trying to install amber9 in fedora10 with gfortan and gcc
>> > compilers.
>> > The compilation stopped with the following error (full error file is
>> > attached). When i searched in amber mail archive, i found that X11-
>> > devel
>> > libraries has to be installed in the system. But X11-devel libraries
>> > are
>> > already installed in my system. Kindly write what is going wrong.
>> >
>> > The error i got is:
>> >
>> > WcActCB.c:1463: error: expected expression before ']' token
>> > WcActCB.c:1536: error: expected '=', ',', ';', 'asm' or '__attribute__'
>> > before 'already'
>> > WcActCB.c:1536: error: 'already' undeclared (first use in this
>> > function)
>> > make[2]: *** [WcActCB.o] Error 1
>> > make[2]: Leaving directory `/usr/local/amber9/src/leap/src/Wc'
>> > make[1]: *** [install] Error 2
>> > make[1]: Leaving directory `/usr/local/amber9/src/leap'
>> > make: *** [serial] Error 2
>> >
>> > output of the command: yum info libX11-devel
>> >
>> > Installed Packages
>> > Name : libX11-devel
>> > Arch : i386
>> > Version : 1.1.5
>> > Release : 4.fc10
>> > Size : 1.1 M
>> > Repo : installed
>> > >From repo : updates
>> > Summary : X.Org X11 libX11 development package
>> > URL : http://www.x.org
>> > License : MIT
>> > Description: X.Org X11 libX11 development package
>> >
>> > Bala
>>
>>
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>>
>
>
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