Ambertools15安装（详细）

这篇博文专门讲述 Ambertools15的安装方法，尽管Ambertools16版本已经正是发行了，但两者在安装方式上没有任何区别。比较偏爱Ambertools15的原因主要还是在容量方面(230M)，它比Ambertools14改进了不少，但其bz2型压缩容量只增加了27M，而Ambertools16已经有330M了(这个新功能如果在以后应用中涉略较多的话，我在专门开博讨论)。网络中对如何安装ambertools较为缺乏，而且介绍非常简单，参考链接[1]和[2]。

在安装时，要了解tools里面的文件多数场合是用不到的，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，上面安装过程过程中，压缩文件的名称依然是Amber14，这是目前还没有改过来。另外，下面的安装方式是错误的：

[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

参考链接：

[1] Amber14安装方法;关于Mac 10.10 安装ambertools 14 心得;Amber11+AmberTools1.5在RHEL5.4中的安装

[2] Amber11+AmberTools1.5+CUDA加速-安装总结;Mac OS 安装Ambertools14;Amber14在Centos6.6下的安装

[3] ubuntu14.04 安装ambertools15;Redhat 5.6中 Amber12的安装;Amber10/Ambertool1.2 Linux安装步骤

[4] Amber12安装-完整;Amber安装并行;Amber11 + AmberTools1.5 软件包和详细安装步骤，附Redhat5.4下载地址

[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发布

[7] Amber tools 中的antechamber 必须要在安装了amber11的前体下才能使用么;amber11+ambertools1.5 安装问题

[8] AMBER10 和AMBERTOOLS-1.2 for linux;使用AmberTools+ACPYPE+Gaussian创建小分子GAFF力场的拓扑文件

[9] 分子模拟软件Amber14.0 单一采购来源公示;Computer-Aided Drug Design;Re: [AMBER] frcmod file erro

[10] 如何利用VMD的topotools工具导出data文件中需要的bond,angle, dihedral list;Re: [AMBER] csh problem

[11] 如何将pdb文件批量转换为mol2格式文件;用VMD画虚线;Re: [AMBER] get sqm Error when run antechamber

[12] AMBER16新功能介绍;AMBER:小分子处理;Re: [AMBER] convergence problem in antechamber with Ambertools14