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