AMBER Archive (2004)

Subject: RE: AMBER: amber8 compilation

From: lucian livadaru (livadluc_at_yahoo.ca)
Date: Mon Nov 22 2004 - 16:22:43 CST

Dear Ross,
 
I had XFree86 version 4.2.0 on my computer at the time of the compilation. What other binaries are required for a complete compilation?
 
 
Here are the contents of my /usr/X11R6/bin

appres fslsfonts mergelib rstart startx xclipboard xfd xkbbell xmag xrefresh xsm

atobm fstobdf mkcfm rstartd texteroids xclock xfindproxy xkbcomp xman xscreensaver xstdcmap

bdftopcf glxgears mkdirhier RunWM twm xcmsdb xfontsel xkbevd Xmark xscreensaver-command xterm

bdftruncate.pl glxinfo mkfontdir RunWM.Fvwm95 ucs2any.pl xconsole XFree86 xkbprint xmessage xscreensaver-demo Xtest

beforelight iceauth mkfontscale RunWM.MWM uxterm xcutsel xfs xkbvleds xmodmap xscreensaver-getimage xvidtune

bitmap ico mkhtmlindex RunWM.WindowMaker viewres xditview xfsinfo xkbwatch xmonisdn xscreensaver-getimage-file xvinfo

bmtoa lbxproxy mkxauth scanpci X xdm xfwp xkill xmtr xscreensaver-getimage-video xwd

cleanlinks listres oclock sessreg x11perf xdpyinfo xgamma xload xon xscreensaver-gl-helper xwininfo

dga lndir pcitweak setxkbmap x11perfcomp xedit xgc xlogo xprop xset xwud

dpsexec luit proxymngr showfont xauth xev xhost xlsatoms Xprt xsetmode

dpsinfo makepsres resize showrgb xbiff xeyes xinit xlsclients xrandr xsetpointer

editres makestrs revpath smproxy xcalc xf86config xisdnload xlsfonts xrdb xsetroot

 
Thanks,
Lucian
 

Ross Walker <ross_at_rosswalker.co.uk> wrote:Dear Lucian,
 
You probably don't have the X11 development libraries installed. XFree86-devel (or xorg-devel in fedora). You need to install the rpm for this since it contains the x11 development libraries and headers that you need for xleap.
 
see: http://amber.ch.ic.ac.uk/archive/200406/0133.html
 
All the best
Ross

/\
\/
|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
| http://www.rosswalker.co.uk/ | PGP Key available on request |

 

---------------------------------
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of lucian livadaru
Sent: 19 November 2004 10:51
To: amber_at_scripps.edu
Subject: AMBER: amber8 compilation

Hello all,

I have been trying to compile amber8 various machines and with different compilers and so far no attempt has been completely successfull. The compilation fails at some point or another.

My latest attempt is a i686 cluster running Linux 2.4.18 -14 smp. I have installed the latest (8.1) fortran and C++ intel compilers. Following the instructions in the manual and on the webpage at http://amber.scripps.edu/cluster_info/index.html, I succeed to partially compile the package. What seems to systematically fail to compile is xLeap.

I used ./configure -ifort before running the make file.

Could anyone help with this problem? Could anyone email my a zip of the amber executables compiled for a similar platform?

Thanks!

Here's some additional information about the outcome:

THE EXECUTABLES CREATED ARE:

-rwxrwxr-x 1 ben ben 846944 Nov 19 13:18 addles

-rwxrwxr-x 1 ben ben 49745 Nov 19 13:19 am1bcc

-rwxrwxr-x 1 ben ben 561453 Nov 19 13:19 ambmask

-rwxrwxr-x 1 ben ben 599652 Nov 19 13:19 ambpdb

-rwxrwxr-x 1 ben ben 766546 Nov 19 13:19 anal

-rwxrwxr-x 1 ben ben 121294 Nov 19 13:20 antechamber

-rwxrwxr-x 1 ben ben 89056 Nov 19 13:20 atomtype

-rwxrwxr-x 1 ben ben 119122 Nov 19 13:20 bondtype

-rwxrwxr-x 1 ben ben 4785 Nov 19 13:19 calcpka.pl

-rw-rw-r-- 1 ben ben 24855 Nov 19 13:19 CPin.pm

-rwxrwxr-x 1 ben ben 4641 Nov 19 13:19 cpinutil.pl

-rwxrwxr-x 1 ben ben 58143 Nov 19 13:20 crdgrow

-rwxrwxr-x 1 ben ben 29354 Nov 19 13:20 database

-rwxrwxr-x 1 ben ben 1754657 Nov 19 13:19 divcon

-rwxrwxr-x 1 ben ben 18107 Nov 19 13:20 espgen

-rwxrwxr-x 1 ben ben 594981 Nov 19 13:19 fantasian

-rwxrwxr-x 1 ben ben 504115 Nov 19 13:19 gwh

-rwxr-xr-x 1 ben ben 28803 Nov 19 13:19 makeANG_RST

-rwxr-xr-x 1 ben ben 5955 Nov 19 13:19 makeCHIR_RST

-rwxrwxr-x 1 ben ben 523786 Nov 19 13:19 make_crd_hg

-rwxr-xr-x 1 ben ben 9594 Nov 19 13:19 makeDIP_RST.dna

-rwxr-xr-x 1 ben ben 3316 Nov 19 13:19 makeDIP_RST.protein

-rwxr-xr-x 1 ben ben 32014 Nov 19 13:19 makeDIST_RST

-rwxr-xr-x 1 ben ben 9234 Nov 19 13:19 makeSHF_RST

-rwxrwxr-x 1 ben ben 2146 Nov 19 13:19 mm_pbsa.pl

-rwxrwxr-x 1 ben ben 1036 Nov 19 13:19 mm_pbsa_statistics.pl

-rwxrwxr-x 1 ben ben 89827 Nov 19 13:19 molsurf

-rwxrwxr-x 1 ben ben 496076 Nov 19 13:18 new2oldparm

-rwxrwxr-x 1 ben ben 1170289 Nov 19 13:19 nmode

-rwxrwxr-x 1 ben ben 470939 Nov 19 13:19 nucgen

-rwxrwxr-x 1 ben ben 28977 Nov 19 13:20 parmcal

-rwxrwxr-x 1 ben ben 96811 Nov 19 13:20 parmchk

-rwxrwxr-x 1 ben ben 1399542 Nov 19 13:19 pbsa

-rwxrwxr-x 1 ben ben 491845 Nov 19 13:19 pol_h

-rwxrwxr-x 1 ben ben 71364 Nov 19 13:20 prepgen

-rwxrwxr-x 1 ben ben 507158 Nov 19 13:19 protonate

-rwxrwxr-x 1 ben ben 1110792 Nov 19 13:19 ptraj

-rwxrwxr-x 1 ben ben 1110792 Nov 19 13:19 rdparm

-rw-rw-r-- 1 ben ben 865 Nov 19 13:20 README

-rwxrwxr-x 1 ben ben 594678 Nov 19 13:19 resp

-rwxrwxr-x 1 ben ben 31256 Nov 19 13:20 respgen

-rwxrwxr-x 1 ben ben 2302353 Nov 19 13:18 sander

-rwxrwxr-x 1 ben ben 2316139 Nov 19 13:19 sander.LES

-rwxrwxr-x 1 ben ben 2852310 Nov 19 13:19 sander.QMMM

-rwxrwxr-x 1 ben ben 8304 Nov 19 13:19 senergy

-rwxrwxr-x 1 ben ben 15475 Nov 19 13:19 sviol

-rwxrwxr-x 1 ben ben 2049 Nov 19 13:19 sviol2

-rwxrwxr-x 1 ben ben 615538 Nov 19 13:20 teLeap

-rwxrwxr-x 1 ben ben 348 Nov 19 13:20 tleap

-rwxrwxr-x 1 ben ben 393 Nov 19 13:20 xleap

 

 

 

THE FINAL SCREEN OF THE COMPILATION PROCESS IS:

 

xaHBondParmTable.c: At top level:

xaHBondParmTable.c:423: parse error before "wCreated"

xaHBondParmTable.c: In function `XAHPTNewPopupTable':

xaHBondParmTable.c:426: `hptPNew' undeclared (first use in this function)

xaHBondParmTable.c:431: parse error before ')' token

xaHBondParmTable.c:431: parse error before ')' token

xaHBondParmTable.c:433: `fCallback' undeclared (first use in this function)

xaHBondParmTable.c:434: `wWidget' undeclared (first use in this function)

xaHBondParmTable.c:435: `psParmSet' undeclared (first use in this function)

xaHBondParmTable.c:440: `wCreated' undeclared (first use in this function)

make[2]: [xaHBondParmTable.o] Error 1 (ignored)

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 -l! S!
 M -lICE
 -lX11 -lm -lpthread

gcc: xTank.o: No such file or directory

gcc: xAction.o: No such file or directory

gcc: xBasics.o: No such file or directory

gcc: xaLeapc.o: No such file or directory

gcc: xaUnitEditor.o: No such file or directory

gcc: xaTable.o: No such file or directory

gcc: xaAtomTable.o: No such file or directory

gcc: XrawRegistr.o: No such file or directory

gcc: xaCommand.o: No such file or directory

gcc: xaTools.o: No such file or directory

gcc: xaAtomParmTable.o: No such file or directory

gcc: xaBondParmTable.o: No such file or directory

gcc: xaAngleParmTable.o: No such file or directory

gcc: xaParmEditor.o: No such file or directory

gcc: xaTorsionParmTable.o: No such file or directory

gcc: xaImproperParmTable.o: No such file or directory

gcc: xaHBondParmTable.o: No such file or directory

gcc: ../Xraw/libXaw.a: No such file or directory

gcc: ../Wc/libWcLeap.a: No such file or directory

gcc: ../Xpm/libXpm.a: No such file or directory

gcc: ../Xmu/libXmu.a: No such file or directory

make[2]: [xaLeap] Error 1 (ignored)

m4 xaLeap.rm4 > XaLeap_wcl

gcc -c -I/usr/X11R6/include -O2 -o tLeap.o tLeap.c

gcc -o teLeap 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 tLeap.o -lm

mv xaLeap teLeap ../../../../exe

mv: cannot stat `xaLeap': No such file or directory

make[2]: [install] Error 1 (ignored)

mv XaLeap_wcl ../../../../dat

make[2]: Leaving directory `/tmp/usr/ben/lucian/amber8/src/leap/src/leap'

Copying shell scripts

cp xleap tleap ../../exe

Copying pixmaps

mkdir ../../dat/pixmap

( cd pixmap ;\

cp `find . -name CVS -prune -o -type f -print ` ../../../dat/pixmap \

)

Finished with the install of LEaP

make[1]: Leaving directory `/tmp/usr/ben/lucian/amber8/src/leap'

Installation of Amber8 (serial) is complete at Fri Nov 19 13:20:41 EST 2004.

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