Amber14  Installation

You can download AmberTools14.tar.bz2 for free, Amber14.tar.bz2 is not free but only featured PMEMD, if you just want to use sander, free version is enough.

1. edit /etc/bashrc
export AMBERHOME=/path/to/amber14

2. untar files

tar xvf AmerTools14.tar.bz2

tar xvf Amber14.tar.bz2

(sudo dnf install libXt-devel libXext-devel libX11-devel libICE-devel libSM-devel   flex patch bzip2-devel zlib-devel on fedora23)

also check tcsh gcc-c++ gcc-gfortran python-devel mpich mpich-devel are properly installed

if you want to install with cuda 7.X with gcc version >4.9

edit the following file and mark off error with "//"

#if __GNUC__ > 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 9)

//#error -- unsupported GNU version! gcc 4.10 and up are not supported!                                       

#endif /* __GNUC__> 4 || (__GNUC__ == 4 && __GNUC_MINOR__ > 9) */

3. configure & compile

3.1 MPI only version

cd /path/to/amber14

./configure -mpi gnu

make sure you source the /../../ before next step

make install


export DO_PARALLEL="mpirun -np 6"(some of the program requires less than 6 threads)
make test.parallel

3.2 Compile with gpu support

export CUDA_HOME=/....

export PATH=$PATH:$CUDA_HOME/bin


./configure -cuda gnu

make install

make test

3.3 If you have more than one graphic card, compile cuda.MPI version

./configure -cuda -mpi gnu

make install

3.4 no matter what compile serial version is a must, so we can get all the tools we need

./configure gnu

make install

make test.seiral





Install matplotlib,Tkinter

yum install python-matplotlib

yum install tkinte


**gcc: error: /usr/lib/rpm/redhat/redhat-hardened-cc1: No such file or directory (fedora 24)


sudo dnf install redhat-rpm-config-40-2.fc24.noarch


amber mdcrd to dcd:

cpptraj -p topology.parm7 -y input.mdcrd -x output.dcd 

to pdb

cpptraj -p water_box.prmtop -y md.rst -x md.pdb

extract frames from mdcrd file

create an input file, *.in

parm morc16_micelle.prmtop
trajin mdcrd 1 300 10
trajout tmp.mdcrd netcdf

cpptraj -i *.in





Amber 2015 Reference Manual