這篇博文專門講述 Ambertools15的安裝方法，盡管Ambertools16版本已經正是發行了，但兩者在安裝方式上沒有任何區別。比較偏愛Ambertools15的原因主要還是在容量方面(230M)，它比Ambertools14改進了不少，但其bz2型壓縮容量只增加了27M，而Ambertools16已經有330M了(這個新功能如果在以后應用中涉略較多的話，我在專門開博討論)。網絡中對如何安裝ambertools較為缺乏，而且介紹非常簡單，參考鏈接[1]和[2]。
在安裝時，要了解tools里面的文件多數場合是用不到的，因此真正有用的是Amber15：
[amber14]$ ./configure gnu
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 15 patches:
update.1 (modifies MMPBSA.py, ParmEd, cpptraj)
update.2 (modifies AmberTools, CUDA)
update.3 (modifies nab, sff)
update.4 (modifies Leap, Lipid14, force, field)
update.5 (modifies ParmEd)
update.6 (modifies pmemd.cuda)
There are patches available. Do you want to apply them now? [y/N] (Recommended Y)
y
Preparing to apply updates... please wait.
Downloading updates for AmberTools 15
Downloading AmberTools 15/update.1 (4.65 KB)
Applying AmberTools 15/update.1
Downloading AmberTools 15/update.2 (2.25 KB)
Applying AmberTools 15/update.2
Downloading AmberTools 15/update.3 (4.09 KB)
Applying AmberTools 15/update.3
Downloading AmberTools 15/update.4 (43.97 KB)
Applying AmberTools 15/update.4
Downloading AmberTools 15/update.5 (798 Bytes)
Applying AmberTools 15/update.5
Downloading AmberTools 15/update.6 (2.46 KB)
Applying AmberTools 15/update.6
NOTE: update_amber only updates the raw source code! You must recompile if you want
any changes to take effect!
Error: /bin/csh not found on your system! Install csh or tcsh and rerun
configure.
Configure failed due to the errors above!
----------------------------------------------------------
[amber14]$ ./configure -help
Error: /bin/csh not found on your system! Install csh or tcsh and rerun
configure.
Configure failed due to the errors above!
[amber14]$ sed -i 's&/bin/csh&/bin/bash&g' `grep -rl /bin/csh ./`
[amber14]$ ./configure --prefix=/home/hongyz/panfile/amber14/build -gnu
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 15 patches:
update.1 (modifies MMPBSA.py, ParmEd, cpptraj)
update.2 (modifies AmberTools, CUDA)
update.3 (modifies nab, sff)
update.4 (modifies Leap, Lipid14, force, field)
update.5 (modifies ParmEd)
update.6 (modifies pmemd.cuda)
There are patches available. Do you want to apply them now? [y/N] (Recommended Y)
N
NOT updating your tree and continuing anyway.
Error: Unknown flag: --prefix=/home/hongyz/panfile/amber14/build
Type './configure -help' for options.
Configure failed due to the errors above!
[amber14]$ ./configure -help
Usage: ./configure [flags] compiler
where compiler is one of: [[ gnu, intel, pgi, or clang ]]
COMPILERS
-----------------------------------
Compiler Set | C | C++ | Fortran
------------------------------------------------
gnu | gcc | g++ | gfortran
intel | icc | icpc | ifort
pgi | pgcc | pgCC | pgf90
clang | clang | clang++ | gfortran
Most common flags:
-mpi Use MPI for parallelization
-cuda Builds the NVIDIA GPU version of pmemd (pmemd.cuda or
pmemd.cuda.MPI) with default SPFP mixed single/double/
fixed-point precision.
(Note: Set CUDA_HOME to your cuda build tools installation
path; this is typically /usr/local/cuda.)
-openmp Use OpenMP pragmas to parallelize NAB, SAXS and paramfit
(not well tested for pgi).
Do not use -openmp and -mpi at the same time. Type "make
clean; make openmp" after setting this flag.
-cygwin Include modifications for cygwin on Windows
-noX11 Do not build programs that require X11 libraries
-macAccelerate Use optimized blas/lapack bundled with Mac OS X
Some influential environment variables:
MKL_HOME If set then link in Intel's MKL libraries (intel, gnu)
For information on less-common flags, type "./configure --full-help"
===============================================================================
[amber14]$ ./configure gnu
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 15 patches:
No patches available
Searching for python2... Found python2.7: /home/hongyz/softvasp/apply/ourpython/bin/python2.7
Obtaining the gnu compiler suite versions, e.g.:
gcc -v
The C version is 4.4.7
The Fortran version is 4.4.7
Testing the gcc compiler:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Testing the g++ compiler:
g++ -fPIC -o testp testp.cpp
OK
Testing the gfortran compiler:
gfortran -fPIC -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
gfortran -fPIC -O0 -c -o testp.f.o testp.f
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c.o testp.f.o -lgfortran -w
OK
Testing pointer size:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Checking NetCDF...
Using bundled NetCDF library.
Starting NetCDF build.
Configuring NetCDF C interface (may be time-consuming)...
Compiling the NetCDF C interface (may be time-consuming)...
Configuring NetCDF Fortran interface (may be time-consuming)...
Compiling the NetCDF Fortran interface (may be time-consuming)...
NetCDF build succeeded.
Checking for zlib:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -lz -o testp testp.c
OK
Checking for libbz2:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -lbz2 -o testp testp.c
OK
Configuring fftw-3.3 (may be time-consuming)...
fftw-3.3 configure succeeded.
Configuring XBLAS (may be time-consuming)...
XBLAS configure succeeded.
Configuring MTK++ (may be time-consuming)...
MTK++-0.2.0 configure succeeded.
The configuration file, config.h, was successfully created.
--------------------------------------------------------------------------------
Environment resource files are provided to set the proper environment
variables to use AMBER and AmberTools. This is required to run any Python
programs (like MMPBSA.py, ParmEd, and MCPB.py)
If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
/home/hongyz/panfile/amber14/amber.sh file in your shell. Consider adding the line
test -f /home/hongyz/panfile/amber14/amber.sh && source /home/hongyz/panfile/amber14/amber.sh
to your startup file (e.g., ~/.bashrc)
If you use a C shell (e.g., csh, tcsh), source the
/home/hongyz/panfile/amber14/amber.csh file in your shell. Consider adding the line
test -f /home/hongyz/panfile/amber14/amber.csh && source /home/hongyz/panfile/amber14/amber.csh
to your startup file (e.g., ~/.cshrc)
--------------------------------------------------------------------------------
The next step is to type 'make install'
Cleaning the src directories. This may take a few moments.
Configure complete.
==============================================================
[amber14]$ ls
amber.csh AmberTools config.h dat include lib logs README src update_amber
amber.sh bin configure doc KNOWN_PROBLEMS lib64 Makefile share test updateutils
--------------------------------------------------------
copying build/scripts-2.7/PdbSearcher.py -> /home/hongyz/panfile/amber14/bin
copying build/scripts-2.7/OptC4.py -> /home/hongyz/panfile/amber14/bin
copying build/scripts-2.7/MCPB.py -> /home/hongyz/panfile/amber14/bin
changing mode of /home/hongyz/panfile/amber14/bin/PdbSearcher.py to 775
changing mode of /home/hongyz/panfile/amber14/bin/OptC4.py to 775
changing mode of /home/hongyz/panfile/amber14/bin/MCPB.py to 775
running install_egg_info
Writing /home/hongyz/panfile/amber14/lib/python2.7/site-packages/pyMSMT-15.0-py2.7.egg-info
Installation of AmberTools14 serial is complete at Tue Nov 29 05:11:24 CST 2016.
make[1]: Leaving directory `/home/hongyz/panfile/amber14/AmberTools/src'
==============================================================
/home/hongyz/panfile/amber14/src/Makefile not found, or -noamber was set.
This is expected if you do not have Amber14.
==============================================================
[amber14]$ ./configure -mpi
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 15 patches:
No patches available
Searching for python2... Found python2.7: /home/hongyz/softvasp/apply/ourpython/bin/python2.7
Error: Architecture/compiler 'unspecified' is not supported!
Type './configure -help' for options.
Configure failed due to the errors above!
-----------------------------------------------------------
注意，上面安裝過程過程中，壓縮文件的名稱依然是Amber14，這是目前還沒有改過來。另外，下面的安裝方式是錯誤的：
[tcsh-6.20.00]$ pwd
/home/hongyz/panfile/tcsh-6.20.00
[tcsh-6.20.00]$ ./configure --prefix=/home/hongyz/panfile/tcsh-6.20.00/build/
[bin]$ pwd
ln -s /home/hongyz/panfile/tcsh-6.20.00/build/bin
[~]$ which bash
/bin/bash
ln -s /home/hongyz/panfile/tcsh-6.20.00/build/bin/tcsh /bin/tcsh
ln -s /home/hongyz/panfile/tcsh-6.20.00/build/bin/tcsh /bin/csh
~/panfile/tcsh-6.20.00/build/bin/tcsh
==================================================================================
make[2]: Leaving directory `/home/hongyz/panfile/amber14/AmberTools/src/sander'
Installation of AmberTools14 MPI is complete at Tue Nov 29 03:48:26 CST 2016.
make[1]: Leaving directory `/home/hongyz/panfile/amber14/AmberTools/src'
==============================================================
/home/hongyz/panfile/amber14/src/Makefile not found, or -noamber was set.
This is expected if you do not have Amber14.
--------------------------------------------------------
export AMBERHOME=/home/hongyz/panfile/amber14
export PATH=$PATH:$AMBERHOME/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$AMBERHOME/lib
export DO_PARALLEL="mpirun -np 16"
make test
(cd AmberTools/test && make test.parallel)
make[1]: Entering directory `/home/hongyz/panfile/amber14/AmberTools/test'
./test_at_parallel.sh
Tests being run with DO_PARALLEL="mpirun -np 16".
Could not import Amber Python modules. This likely means
that your Amber Python environment was not set up correctly
We recommend adding the line:
test -f /home/hongyz/panfile/amber14/amber.sh && source /home/hongyz/panfile/amber14/amber.sh (sh/bash/zsh)
or
test -f /home/hongyz/panfile/amber14/amber.csh && source /home/hongyz/panfile/amber14/amber.csh (csh/tcsh)
to your login shell resource file (e.g., ~/.bashrc or ~/.cshrc)
make[1]: *** [test.parallel] Error 1
make[1]: Leaving directory `/home/hongyz/panfile/amber14/AmberTools/test'
make: *** [test.parallel] Error 2
參考鏈接：
[1] Amber14安裝方法;關於Mac 10.10 安裝ambertools 14 心得;Amber11+AmberTools1.5在RHEL5.4中的安裝
[2] Amber11+AmberTools1.5+CUDA加速-安裝總結;Mac OS 安裝Ambertools14;Amber14在Centos6.6下的安裝
[3] ubuntu14.04 安裝ambertools15;Redhat 5.6中 Amber12的安裝 ;Amber10/Ambertool1.2 Linux安裝步驟
[4] Amber12安裝-完整;Amber安裝並行;Amber11 + AmberTools1.5 軟件包和詳細安裝步驟，附Redhat5.4下載地址
[5] Installing Amber14 And AmberTools15;Re: [AMBER] amber14 CUDA GPU for workstation
[6] Re: [AMBER] errors in plumed and amber14 patch (Jason Swails); Amber12及AmberTools12發布
[7] Amber tools 中的antechamber 必須要在安裝了amber11的前體下才能使用么;amber11+ambertools1.5 安裝問題
[8] AMBER10 和AMBERTOOLS-1.2 for linux;使用AmberTools+ACPYPE+Gaussian創建小分子GAFF力場的拓撲文件
[9] 分子模擬軟件Amber14.0 單一采購來源公示;Computer-Aided Drug Design;Re: [AMBER] frcmod file erro
[10] 如何利用VMD的topotools工具導出data文件中需要的bond,angle, dihedral list;Re: [AMBER] csh problem
[11] 如何將pdb文件批量轉換為mol2格式文件;用VMD畫虛線;Re: [AMBER] get sqm Error when run antechamber
[12] AMBER16新功能介紹;AMBER:小分子處理;Re: [AMBER] convergence problem in antechamber with Ambertools14