AMBER Archive (2008)

Subject: Re: AMBER: Error while compiling Amber

From: David A. Case (
Date: Thu Feb 07 2008 - 19:42:31 CST

On Thu, Feb 07, 2008, Lili Peng wrote:
> *$ ./configure -p4 ifort_x86_64*

What kind of machine are you compiling on? On the one hand, you say "-p4"
(which is for Pentium IV), yet you also say x86_64, which is a very different
type of architecture.

Typing "uname -m" should give you the information you need. Then choose the
correct options.

> *$ ./configure -p4 ifort_ia32 *
> yacc parser.y
> make[2]: execvp: yacc: Permission denied

It looks like you got a lot further this time, so my guess is that you are on
an ia32 (aka i386 aka i686) system. You should see that sander and lots of
other programs have been compiled. For the above problem:

First, try "which yacc" and try to find out if it exists, and if so, why
    you are getting permission denied.

Second, try "which bison": if it looks like you have permissions to run bison,
add the line

YACC = bison -y

to your config.h file (in $AMBERHOME/src).

Or, if neither work, put the attached parser.c file in
$AMBERHOME/src/leap/src/leap, and try again.


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