RE: May I get you help from new user of amber?

From: Yong Duan <>
Date: Mon, 9 Jun 2003 11:12:41 -0400

Dear Mr. Wu,

$AMBERHOME refers to an environmental variable pointing to the directory
where you installed the AMBER package.

"csh, tcsh" refers to your "shell" where you execute a command.
By default, Linux sets you to "bash". If you (or your system
administrator) have not changed anything, bash should be the "shell". In
which case, try

export AMBERHOME="the_directory_where_you_installed_amber".

In Unix, "set" only works for a local variable; "setenv" works for
"environmental" variable. The difference is that the formal works but
the later does not (for AMBER) because environmental variables are
inherited by child processes.

You probably need to read a bit about Linux (or Unix in general), which
is a bit more complicated than, say, Windows.

Good luck!

-----Original Message-----
From: Wu Yingliang []
Sent: Monday, June 09, 2003 10:22 AM
Subject: May I get you help from new user of amber?


Much sorry to disturb you by this email.

I am a new user of amber7 which I got last week. There are some
difficulties during amber7 installing in the Red Hat Linux 9 of my PC,
and I expect your warm-hearted help. The questions are as following:

1> unpack step: "gunzip -c amber7.tgz | tar xvf-" can not be run, my pc
displays "tar: old option 'f' requires an argument ".
   Then I did it by "gunzip -c amber.tgz | tar xv-". And amber7 was
unpacked successfully. However, I am not sure whether amber7 will run

2> after unpacking, there is no directory "$AMBERHOME" in the installing
manual, which I need create? Or and it refers to amber7 which needs to
rename? Directories of "test", "src" etc. in the path "usr/amber7".

3> During setting up $AMBERHOME environment variable:
    Using csh, tcsh, etc: setenv AMBERHOME /usr/local/amber7
    There is no command "setenv" in Red Hat Linux 9, then I use "set"
command instead of "setenv", there is effect on successful installing ?

4> After compiling everything, programs of leap, nmode and antechamber
can not be tested, some messages display

    cd leap; xmkmf
    /bin/sh: line 1: xmkmf: command not found
    make: *** [install] Error 127

Looking forward to getting your help!

Thank you very much in advance!

Best Regards,

Wu Yingliang
College of Life Sciences
Wuhan University
Wuhan 430072
Received on Mon Jun 09 2003 - 16:53:01 PDT
Custom Search