RE: AMBER: tleap load pdb file

From: xiaowen <xwfang.iastate.edu>
Date: Mon, 7 Feb 2005 21:52:36 -0600 (CST)

Dear Ross,
Thanks for your response!

> Can you please send me all of the specs of your
> machine, operating system and version. Compiler and version?

Here are the versions,
% lslpp -h bos.rte 4.3.2.0 (machine installed 1998!)
% lslpp -h xlfcmp 7.1.1.1 (but compilers are newer...)
% lslpp -h vac.C 5.0.1.0 (C)
% lslpp -h vacpp.cmp.C 5.0.0.0 (C++)
% lslpp -h essl.rte.common 3.1.1.0 (DGEMM, etc. math library)

machine is IBM-AIX, Operation system is UNIX
xlf for fortran, xlc for C, xlC for C++

> Amber version + which bug fixes have been applied.
AMBER8 with bugfix.all downloaded from http://amber.scripps.edu/bugfixes80.html
execute:
cd $AMBERHOME
patch -p0 -N -r patch_rejects <bugfix.all

> Create a new directory for amber. E.g.
> Amber8_test and put a "fresh" copy of amber8 in that directory.
> Then copy in the config.h file I have attached to this email into the src
> directory of the new amber 8 installation. YOU WILL NEED TO MODIFY THE
> AMBERHOME LINE OF THIS FILE (at the top) TO POINT TO THE DIRECTORY OF THIS
> AMBER8 INSTALLATION. I have assumed you have an AIX machine with the xlf
> compilers.
> The cd to the src directory and do
> make clean
> make

Today, I followed the instruction to recompile amber8. But cannot finish "make"
(1) I used the same fold name "amber8" and change the old one to amber;
(2) then copy config.h to $AMBERHOME/src, change:
AMBER_SRC=/nsfchem/xwfang/amber8/src (the path is the one generated
by ./configure command)
(3)make clean >& try01.log &
(4)make >& try.log &

the try01.log and try.log were attached with this email!

Thanks, if you need more information, don't hesitate, just let me know!
all the best!

Xiaowen





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Received on Tue Feb 08 2005 - 04:53:01 PST
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