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

From: Guanglei Cui <>
Date: Mon, 9 Jun 2003 10:41:07 -0400

Hi, Yingliang,
     If you're familiar with linux and basic shell, some of problems you
mentioned can be avoided.

On Monday 09 June 2003 10:21, Wu Yingliang wrote:
> 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 correctly.

you should use "gunzip -c amber7.tgz | tar xvf -". the space before '-' makes
the difference. or you can simply use "tar zxvf amber7.tgz".

> 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".

$AMBERHOME is not a directory name, but a environment variable. it just points
to your amber directory. if you installed amber into your home directory, you
can set $AMBERHOME to $HOME/amber7

> 3> During setting up $AMBERHOME environment variable:
> Using csh, tcsh, etc: setenv AMBERHOME /usr/local/amber7

the default SHELL is bash, you can make sure of that by "echo $SHELL". in
bash, you use "export AMBERHOME=<whatever your amber path is>"

> 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

I don't know what package owns xmkmf, but it might be just because it's not on
your search path.

> 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
> 2003-06-09
> ==================================
> College of Life Sciences
> Wuhan University
> Wuhan 430072
> China
> Email:
> ==================================

Guanglei Cui
Dept. of Chemistry
SUNY at Stony Brook
Stony Brook, NY 11790
Received on Mon Jun 09 2003 - 15:53:01 PDT
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