Re: AMBER: Compiling AMBER 9 on windows XP using cygwin

From: Emilio Xavier Esposito <>
Date: Thu, 06 Jul 2006 08:40:39 -0500

Hi Gobind
I used the following commands to compile the serial version of Amber 9
on my Windows XP box using cygwin and g95 (pmemd was not compiled). The
test sets completed with minimal deviations. I only use the Windows
version to set up simulations (remember to use dos2unix once you've
moved the data to the *nix machine) and analyze trajectories.

You should also read David Case's comments about running Amber on
Windows .

Hope this helps

1. go to and download latest set of binaries (cygwin x86
tarball) into c:/temp
(link to the g95 compilers: )
2. open a cygwin bash shell (startx type)
3. cd / (cygwin root)
4. tar zxvf /cygdrive/c/temp/g95-x86-cygwin.tgz
5. cd /cygdrive/c
6. tar zxvf /cygdrive/e/amber9.tgz (e is my CD drive)
7. export AMBERHOME=/cygdrive/c/amber9
9. wget (latest amber9
10. patch -p0 -N -r patch_rejects <bugfix.all
11. cd src
12. ./configure -p4 -cygwin g95
13. make serial
14. ../test
15. make test.serial

Gobind Bisht wrote:
> hi all,
> can anyone sugest how to compile AMBER9 in windows XP. I used cygwin
> but it's not able to find the MKL libraries inspite of the fact that the
> 'lib' path in system environment variables was set to the right location
> of MKL libraries. I had also set LD_LIBRARY_PATH to the mkl libraries in
> the user variablels but the error continues.Whoat should i do? Also the
> "make serial" command is not recognised by cygwin. what command has to
> be used to compile AMBER after making the config.h file?
> Please help
> thanx in advance
> --
> Gobind Singh Bisht
> Department Of Biotechnology
> IIT Kharagpur, Kharagpur-721302
> West Bengal,

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Received on Sun Jul 09 2006 - 06:07:13 PDT
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