AMBER: problem in compiling amber9 and running amber9

From: Prem Prakash Pathak <>
Date: Sat, 21 Jul 2007 17:57:18 +0530

I am working on LINUX SuSE 9.1 .I have amber9 package. I have g95
compiler.To check i do this
drinmr1.drinmr1:~> g95
g95: no input files

so i think that g95 compiler is loaded.
Now to set environment on bash shell

drinmr1.drinmr1:~> AMBERHOME=/home/drinmr1/amber9
drinmr1.drinmr1:~> export AMBERHOME
drinmr1.drinmr1:~> set PATH=$AMBERHOME/exe
drinmr1.drinmr1:~> cd $AMBERHOME/src
drinmr1.drinmr1:~/amber9/src> ./configure g95
AMBERHOME is set to /home/drinmr1/amber9
Setting up Amber configuration file for architecture: g95
Using parallel communications library: none
The MKL_HOME environment variable is not defined.
The configuration file, config.h, was successfully created.
drinmr1.drinmr1:~/amber9/src> make serial

I get a list of violation which i do not know how to intepret.
I can not past all the errors,I am pasting below some of them.
WcActCB.c: In function `WcCreatePopupsACT':
WcActCB.c:1432: error: parse error before "XEvent"
WcActCB.c:1432: error: parse error before "Cardinal"
WcActCB.c:1536: error: parse error before '}' token
WcActCB.c:1538: error: parse error before '(' token
WcCreateP.h:253: warning: array `wcWidgetCvtArgs' assumed to have one element

make[2]: *** [WcActCB.o] Error 1
make[2]: Leaving directory `/home/drinmr1/amber9/src/leap/src/Wc'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/home/drinmr1/amber9/src/leap'
make: *** [serial] Error 2
drinmr1.drinmr1:~/amber9/src> cd $AMBERHOME/test
drinmr1.drinmr1:~/amber9/test> make test.serial

here also i get some failure messages

cd qmmm2/MG_QM_water_MM_AM1_periodic; ./Run.notimaged_md
diffing with mdout.notimaged_md
possible FAILURE: check mdout.notimaged_md.dif
cd bintraj; ./Run.bintraj

sander and ptraj: test sander netCDF output and ptraj netCDF input
  ./Run.bintraj: Program error
make: [test.sander.BASIC] Error 1 (ignored)
cd gb_rna; ./Run.gbrna
diffing with mdout.gbrna

and finally i get these error

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

Now the in
it doesnot have leap executable nor xleap. But it has one runleap
I do not understand what is going on.
if i give
drinmr1.drinmr1:~/amber9/exe> runleap
bash: runleap: command not found
cdrinmr1.cdrinmr1:~/amber9/exe> $runleap
cdrinmr1.cdrinmr1:~/amber9/exe> $leap

Please help me in running it.
I was working with cyana, so i have all my file formats in cyana
format, I have *.upl, *.aco, and *.pdb file.
I want to do energy minimization on my structure with amber9, but i am
not able to do it.
In fact i am not able to move a single step to it.
Prem Prakash Pathak
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Received on Sun Jul 22 2007 - 06:07:59 PDT
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