Installing Amber12 and AmberTools 13 on CentOS 6.3

# yum install flex

# cd /BiO/apps

# tar jxvfp Amber12.tar.bz2

# tar jxvfp AmberTools12.tar.bz2

# cd amber12

# export AMBERHOME=`pwd`

# export CUDA_HOME=/BiO/apps/cuda/

# ./patch_amber.py --update

Determining patches to download for AmberTools12

  Downloading bugfix.14

  Downloading bugfix.15

  Downloading bugfix.16

  Downloading bugfix.17

  Downloading bugfix.18

  Downloading bugfix.19

  Downloading bugfix.20

  Downloading bugfix.21

  Downloading bugfix.22

  Downloading bugfix.23

  Downloading bugfix.24

  Downloading bugfix.25

  Downloading bugfix.26

  Downloading bugfix.27

  Downloading bugfix.28

  Downloading bugfix.29

  Downloading bugfix.30

  Downloading bugfix.31

  Downloading bugfix.32

  Downloading bugfix.33

  Downloading bugfix.34

  Downloading bugfix.35

  Downloading bugfix.36

  Downloading bugfix.37

Determining patches to download for Amber12

  Downloading bugfix.1

  Downloading bugfix.2

  Downloading bugfix.3

  Downloading bugfix.4

  Downloading bugfix.5

  Downloading bugfix.6

  Downloading bugfix.7

  Downloading bugfix.8

Applying AmberTools12 patches

  Moving bugfix.14 to AmberTools_Applied_Patches

  Moving bugfix.15 to AmberTools_Applied_Patches

Creating file /BiO/apps/amber12/AmberTools/src/cpptraj/src/Action_AutoImage.cpp

Creating file /BiO/apps/amber12/AmberTools/src/cpptraj/src/Action_AutoImage.h

  Moving bugfix.16 to AmberTools_Applied_Patches

  Moving bugfix.17 to AmberTools_Applied_Patches

  Moving bugfix.18 to AmberTools_Applied_Patches

  Moving bugfix.19 to AmberTools_Applied_Patches

  Moving bugfix.20 to AmberTools_Applied_Patches

  Moving bugfix.21 to AmberTools_Applied_Patches

This patch patches patch_amber.py. I will quit after this patch so the rest may be applied with the updated version.

  Moving bugfix.22 to AmberTools_Applied_Patches

Basic AmberTools 12 + Amber 12 install (Serial)

# ./configure gnu

Checking for updates...

AmberTools12 has 15 unapplied patches: 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37

Amber12 has 17 unapplied patches: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17

There are patches available. Do you want to apply them now? [y/n] (Recommended Y)

y

...

...

...

# make -j 8 install

Building AmberTools 12 and Amber 12 in parallel

# cd $AMBERHOME

# ./configure -mpi gnu

# make install

Building CUDA-enabled Amber 12 (pmemd.cuda Amber 12 only!)

# cd $AMBERHOME

# ./configure -cuda gnu

# make install

Building CUDA-enabled Amber in parallel

# cd $AMBERHOME

# ./configure -cuda -mpi gnu

# make install