AMBER: problem with AMBER8 installation

From: Subhasish Chatterjee <>
Date: Wed, 7 Feb 2007 12:50:48 -0500


I am facing problem to install AMBER 8.

We have a Precision Workstation 390n Intel(
Core(tm)2 Duo E6700 2.66GHz/1066MHz/4MB
L2/Dual-core/VT, Red Hat Enterprise Linux WS v4 for
EM64T 64bit system w/ 3 YR RHN, w/ Media ) with
Graphics Card(: 512MB PCIe x16 nVidia Quadro FX 4500,
Dual Monitor DVI or VGA) and two hard drives (500GB
SATA 3.0Gb/s with NCQ and 16MB DataBurst Cache&#153.

I have Intel Fortran 90 compiler (ifort)

I logged in as root and downloaded the amber8
[/usr/local/] from CD.

I exported the path in the .bash_profile file of root.

[ export AMBERHOME =/usr/local/amber8
  export PATH]


2. patch p0 N r patch_rejects < bugfix.all ( going
3. cd $AMBERHOME/src
4. ./configure ifort (giving config,h file )
5. make serial ( it fails, giving error message )

I tried the above steps by the following way also

2. patch p0 N r patch_rejects < bugfix.all ( going
3. cd $AMBERHOME/src
4. ./configure p4 ifort (giving config,h file )
5. make serial ( giving error)

I also tried without patching the bugfix.all, but no
results .
Only if I use make i command , then it goes with out
error but fails in the next step.

The errors are as follows ...

ake[2]: Entering directory `/usr/local/AMBER8/amber8/src/leap/src/leap'
Makefile:4: warning: overriding commands for target `.c.o'
../../../config.h:87: warning: ignoring old commands for target `.c.o'
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 -lXt
collect2: ld returned 1 exit status
make[2]: *** [xaLeap] Error 1
make[2]: Leaving directory `/usr/local/AMBER8/amber8/src/leap/src/leap'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/usr/local/AMBER8/amber8/src/leap'
make: *** [serial] Error 2

Please advise how to install AMBER 8 properly in this system.
I would greatly appreciate any help.

Thank you,
Subhasish Chatterjee
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Received on Sun Feb 11 2007 - 06:07:09 PST
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