amber16编译安装

2021.12.1更新

    明白了，同质性隐式膜MMPBSA方法在AmberTools17上开始实现，异质性隐式膜在AmberTools19以及以上版本才有。

    如果不是为了使用pmemd.cuda，AMBER是不需要编译安装的。AMBER官网（http://ambermd.org/GetAmber.php#ambertools）提供了三种安装AmberTools的方法

    我喜欢Option2，直接使用conda 安装AmberTools：

Option 2: Binary distribution via conda

The conda package-management system can install a serial, binary (pre-compiled) distribution. This should work for Linux and MacOS systems, and may be sufficient for many users. It provides a simple way to get started with AmberTools, and to install it into many workflows. It does not provide access to parallel or GPU-enabled options, and the full source-code distributions are needed if you wish to combine AmberTools with Amber.

To install, proceed as follows:

• If you don't have conda installed, please visit the Miniconda download page.

• Those with an existing conda installation may wish to create a new conda "environment" to avoid conflicts with what you already have installed. To do this:

    conda create --name AmberTools21
    conda activate AmberTools21

  (Note that you would need to perform the "conda activate" step every time you wish use AmberTools21 in a new terminal; it might be appropriate to add this to your start-up script. Creating a new environment should not be necessary if you only use conda for AmberTools.)

• Once this is done, type:

    conda install -c conda-forge ambertools=21 compilers

• AmberTools is updated from time to time. To keep your conda package up-to-date, do this:

    conda update -c conda-forge ambertools

Thanks to Jaime Rodríguez-Guerra, the Chodera lab, and Simon Bray for spearheading this.

    这样安装的AmberTools可以在使用的时候，执行conda activate Ambertools21即可切换到AmberTools21环境。

    我这里安装的是AmberTools20，安装之后运行出现一些问题，解决问题的后续操作大概有：

    （1）conda安装mpi4py；     conda install -c conda-forge mpi4py

      一般到这里就解决了MMPBSA.py.MPI的问题。

    （2）如果没有，可以尝试设置MMPBSA.py和MMPBSA.py.MPI的python环境为本机conda创建的python2环境，然后将MMPBSA以及MMPBSA.py.MPI的运行脚本改为python2的格式。

(AmberTools20) ruichaomao@io:anaconda3$ diff envs/AmberTools20/bin/MMPBSA.py.MPI ~/.software/Amber16/amber16/bin/MMPBSA.py.MPI
1c1
< #!/home5/ruichaomao/.software/anaconda3/envs/AmberTools20/bin/python
---
> #!/home5/ruichaomao/.software/anaconda3/envs/python2/bin/python
71c71
< except CommandlineError as e:
---
> except CommandlineError, e:
91c91
<    except InputError as e:
---
>    except InputError, e:
    改好后即可运行隐式膜MMPBSA.py！

centos服务器安装amber16：

！！！终于发现了为什么我安装的MMPBSA.py没有膜的参数，因为膜的参数只有更新版才有，需要在./configure之前首先升级AmberTools17的版本，

解压后首先执行 ./update_amber --update和 ./update_amber --upgrade。最后安装成功的完整命令如下：

 1169  ./update_amber --update
 1170  ./update_amber --upgrade
 1171  ./configure --with-python /home5/ruichaomao/.software/anaconda3/envs/python2/bin/python gnu
 1172  ls
 1173  source amber.sh
 1174  make install
 1175  ls
 1176  ./bin/MMPBSA.py
 1177  ./bin/MMPBSA.py  --input-file-help