AMBER: Troubles installing amber

From: Margaret Doll <>
Date: Fri, 7 Dec 2007 14:47:26 -0500

I have an SGI cluster running Centos 2.6.9-42 and Rocks 4.2.1. I am
not interested in installing the software to run in parallel on the

I untarred the amber9 files into /state/partition1/apps/amber9
I copied the bugfix.all files off the web pages to

patch -p0 -N -r patch_rejects < amberpatches

I was required to provide a name of the file to be modified for
line 18066 in amberpatches.

I provided /state/partition1/apps/amber9/src/sander/runmd.f

The results of the patch replacements were
  more patch_rejects
*** 814,820 ****
      iprint = 0
      if( nstep == 0 .or. nstep+1 == nstlim ) iprint = 1
      ! TIME_force is started and stopped inside force
      call force(xx,ix,ih,ipairs,x,f,ener(23),vir, &
            xx(l96),xx(l97),xx(l98),xx(l99), qsetup,qpsander, &
--- 814,825 ----
      iprint = 0
      if( nstep == 0 .or. nstep+1 == nstlim ) iprint = 1
      ! TIME_force is started and stopped inside force
! #ifdef MPI
! if( initremd ) then
! irespa = 0
! end if
! #endif
      call force(xx,ix,ih,ipairs,x,f,ener(23),vir, &
            xx(l96),xx(l97),xx(l98),xx(l99), qsetup,qpsander, &

export AMBERHOME=/state/partition1/apps/amber9
cd src
./configure pgf90
make serial

pdbFile.c: In function `writeTER':
pdbFile.c:1761: warning: initialization from incompatible pointer type
gcc -c -I/usr/X11R6/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE
-O2 -m32 -o tools.o tools.c
tools.c: In function `iToolDistanceSearch':
tools.c:1643: warning: passing arg 1 of `SortByDouble' from
incompatible pointer type
tools.c:1643: warning: passing arg 4 of `SortByDouble' from
incompatible pointer type
tools.c: In function `ToolOrientPrincipleAxisAlongCoordinateAxis':
tools.c:1714: warning: passing arg 2 of `MathOpDiagonalize' from
incompatible pointer typegcc -c -I/usr/X11R6/include -
D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -O2 -m32 -o variables.o
yacc parser.y
make[2]: yacc: Command not found
make[2]: *** [parser.c] Error 127
make[2]: Leaving directory `/state/partition1/apps/amber9/src/leap/src/
make[1]: *** [install] Error 2
make[1]: Leaving directory `/state/partition1/apps/amber9/src/leap'
make: *** [serial] Error 2

make test.serial fails with
ptraj: test ptraj on averaging les trajectory to normal trajectory
diffing with hef_averaged.crd
cd leap; ./Run.tleap
  Error: ./tleap -> ../../exe/teLeap does not exist
make: *** [test.leap] Error 1

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Received on Sun Dec 09 2007 - 06:07:43 PST
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