[AMBER] RE: About amber10 installation

From: Ross Walker <ross.rosswalker.co.uk>
Date: Sat, 13 Mar 2010 10:22:44 -0800

Dear Navanath,


Such questions should go to the AMBER mailing list where I am copying this.
See http://lists.ambermd.org/ for signup details.


The procedure you use below is somewhat confused. I would do the following.


>From a clean directory.


The following assumes you are installing in your home directory.


Step i) Edit users (or /etc/bashrc) and add:


                export AMBERHOME=~/amber10/

                export PATH=$AMBERHOME/exe/:$PATH


ii) cd ~


Copy AmberTools1.2.tar.bz2 to this directory

Copy Amber10.tar.bz2 to this directory


iii) tar xvjf AmberTools-1.2.tar.bz2

      tar xvjf Amber10.tar.bz2


iv) Patch the source directory with bugfixes.


wget http://ambermd.org/bugfixes/AmberTools/1.2/bugfix.all

patch -p0 <bugfix.all

rm -f bugfix.all

wget http://ambermd.org/bugfixes/10.0/bugfix.all

patch -p0 <bugfix.all


v) cd src


vi) ./configure_at gcc


vii) make -f Makefile_at


viii) cd $AMBERHOME/test


iix) make -f Makefile_at test


check TEST_FAILURES.diff


ix) cd $AMBERHOME/src/


x) ./configure_amber gfortan


xi) make serial


xii) cd $AMBERHOME/test/


xiii) make test


xiv) make test.QMMM


Same as above - check TEST_FAILURES.diff


Good luck,



From: Navanath Kumbhar [mailto:nmkumbhar.gmail.com]
Sent: Saturday, March 13, 2010 8:08 AM
To: ross.rosswalker.co.uk
Subject: About amber10 installation


Dear Sir,


I have tried to install amber10 on Redhat5.

I have followed all procedure from INSTALL as given below


tar xvjf AmberTools -1[1].2.tar.bz2


tar xvjf Amber10[1].tar.bz2

set path for bash shell


1. AMBERHOME=/usr/local/amber10

    export AMBERHOME


2. cd $AMBERHOME/src

   ./configure_at gcc

3. make -f Makefile_at


4. cd $AMBERHOME/test:

    make -f Makefile_at test

5. set path =/usr/local/amber10/exe /usr/local/amber10/bin (executable
path- from ambertool.pdf)



 patch -p0 -N -r patch-rejects < bugfix.all


7. cd $AMBERHOME/src

 ./configure_amber gfortran


i had edit configure_amber.h


AMBERBUILDFLAGS= "-I/usr/local/amber10/include"



8.cd $AMBERHOME/exe


 make serial


make: *** No rule to make target 'serial. stop.


So please suggest me how edit the configure.h file and how to run make
serial commands.

 I am eagerly waiting for your reply.



Thanking You,


Navanath Kumbhar

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Received on Sat Mar 13 2010 - 10:30:03 PST
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