Re: AMBER: hi

From: Ilyas Yildirim <>
Date: Wed, 14 Feb 2007 17:14:11 -0500 (EST)

Dear Anju,

I think you are not familiar with unix system. It will be better if you
get a unix book and try to understand the logic of it (I know, when I
first started using SUSE Linux, it was pretty different. You expect it
to look like XP, but it is not. Once you get used to it, you wont go back
to XP, though. :)).

First thing about your question, did u install the AMBER package without
error? If yes, did you do the 'test' part of the installation? If you did
everything till this point, and did not get any error messages, I would
guess that you need to initialize the necessary libraries, /bin points to
your shell. Which shell are you using? Just as an example, I am using the
tcsh and in my .tcshrc file (under your $HOME directory), I defined the
following variables:

# .tcshrc

setenv PATH "/usr/local/bin:/usr/local/sbin:/usr/sbin:/sbin:${PATH}:./"
setenv LD_LIBRARY_PATH /usr/local/lib

# AMBER 9 stuff
setenv AMBERHOME ~/amber9
setenv PATH "${AMBERHOME}/exe:${PATH}"

# MPICH - Parallel Communication
setenv MPICH_HOME ~/mpich
setenv PATH "${MPICH_HOME}/bin:${PATH}"

# Intel Fortran Compiler 9.0
source ~/intel/cc/9.0/bin/iccvars.csh
source ~/intel/fc/9.0/bin/ifortvars.csh


Depending on which shell you are using (bash/c-shell/etc.), you need to
define the variables necessary for the AMBER programs. DO NOT copy/paste
the above example, because I am sure your system is different. Find where
amber9 is installed in the system, and define the AMBERHOME variable.
Then, find where mpich/mpi is installed, and define this in your shell
script. Finally, find where intel fortran compiler is installed and define
this variable. What the above script does is, whenever you login to your
account, these variables will be defined instantly. Remember, when you
installed the amber 9 suite, you had to define AMBERHOME (setenv AMBERHOME
/usr/local/amber9 - in tcsh/csh).

Hope this can help you a little bit. Good luck.

On Tue, 13 Feb 2007, Anju Sharma wrote:

> Hello Steven Sir,
> as directed by you i set the path of AMBERHOME. What i did is as follows:
> >echo $AMBERHOME
> ----------nothing appears----------
> >export AMBERHOME = /usr/local/amber8
> >echo $AMBERHOME
> /usr/local/amber8
> >cd exe
> >ls
> nucgen exe appears in list........
> >$AMBERHOME/exe/nucgen -O -i -o nuc.out -d
> $AMBERHOME/dat/leap/parm/nucgen.dat -p nuc.pdb
> /usr/local/amber8/exe/nucgen: error while lloading shared libraries:
> :cannot open shared object file: no such file or directory.
> this is wht i got wht should i do nw.
> sorry for bothering u agn....
> Anju
> On 2/13/07, Steven Winfield <> wrote:
> >
> > Hi,
> >
> > Try typing:
> >
> > echo $AMBERHOME
> >
> > and if nothing is printed then you need to set the AMBERHOME environment
> > variable using (in the bash shell)
> >
> > export AMBERHOME=/path/to/your/amber/installation
> >
> > (obviously with your AMBER directory after the = sign)
> >
> > Then try running the command again. If you use bash as your shell it
> > might be worth adding that line to your .bashrc file (again, if using
> > bash) or similar.
> >
> > Regards,
> >
> > Steve.
> >
> >

  Ilyas Yildirim
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-
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Received on Sun Feb 18 2007 - 06:07:11 PST
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