AmberTools24安装时miniforge的问题

milk_q

求助一下大家，我在安装Amber24和Ambertools24时，已经在github下载好miniforge3并放到~/AmberTools24/amber24_src/build/CMakeFiles/miniconda/download目录下
但是在执行run_cmake时还是重新在官网下载了，并提示：

Successfully installed pip-25.2
Channels:
- conda-forge
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/main
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/pkgs/free
- https://mirrors.tuna.tsinghua.edu.cn/anaconda/cloud/conda-forge
Platform: linux-64
Collecting package metadata (repodata.json): ...working... Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst

Retrying (Retry(total=1, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")': /conda-forge/noarch/repodata.json.zst

求助一下大家这是怎么回事

abin

字面意思

Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after connection broken by 'ReadTimeoutError("HTTPSConnectionPool(host='conda.anaconda.org', port=443): Read timed out. (read timeout=9.15)")'

你可以致电网络运营商，
询问，这个错误如何解决？

或者向工信部投诉，
网络存在问题，导致科研工作无法开展？

通俗讲， 网络超时，无法访问。

原因就很多了。。。。

八月的雨季

安装包名字改一下

Huschein

Amber的conda环境不需要那么复杂，你只需要自己建好一个conda环境，python 大概3.9就行，然后自行conda install numpy matplotlib scipy等关键包之后，在执行run_cmake之前，切到对应的conda环境，然后把download conda那个选项改为false，Amber会自动寻找本地的conda环境

milk_q

Huschein 发表于 2025-8-8 16:49
Amber的conda环境不需要那么复杂，你只需要自己建好一个conda环境，python 大概3.9就行，然后自行conda ins ...

好的 谢谢您 我改了一下安装的最新的pmemd24+ambertools25按照官网的手册 在修改run_cmake里的-DMPI=TRUE，-DOWNLOAD_MINICONDA=FALSE,但是报错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, MCPB.py, and pytraj)
--
-- If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
-- /home/jingjie/pmemd24//amber.sh file in your shell. Consider adding the line
--   test -f /home/jingjie/pmemd24//amber.sh && source /home/jingjie/pmemd24//amber.sh
-- to your startup file (e.g., ~/.bashrc)
--
-- If you use a C shell (e.g., csh, tcsh), source the
-- /home/jingjie/pmemd24//amber.csh file in your shell. Consider adding the line
--   test -f /home/jingjie/pmemd24//amber.csh && source /home/jingjie/pmemd24//amber.csh
-- to your startup file (e.g., ~/.cshrc)
--
-- Amber will be installed to /home/jingjie/pmemd24/

If errors are reported, search for 'CMake Error' in the cmake.log file. 请问这是什么原因我已经配置了pmemd24的source环境

milk_q

abin 发表于 2025-8-8 10:50
字面意思

Retrying (Retry(total=2, connect=None, read=None, redirect=None, status=None)) after con ...

好的 谢谢您 我改了一下安装的最新的pmemd24+ambertools25按照官网的手册 在修改run_cmake里的-DOWNLOAD_MINICONDA=FALSE,但是报错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, MCPB.py, and pytraj)
--
-- If you use a Bourne shell (e.g., bash, sh, zsh, etc.), source the
-- /home/jingjie/pmemd24//amber.sh file in your shell. Consider adding the line
--   test -f /home/jingjie/pmemd24//amber.sh && source /home/jingjie/pmemd24//amber.sh
-- to your startup file (e.g., ~/.bashrc)
--
-- If you use a C shell (e.g., csh, tcsh), source the
-- /home/jingjie/pmemd24//amber.csh file in your shell. Consider adding the line
--   test -f /home/jingjie/pmemd24//amber.csh && source /home/jingjie/pmemd24//amber.csh
-- to your startup file (e.g., ~/.cshrc)
--
-- Amber will be installed to /home/jingjie/pmemd24/

If errors are reported, search for 'CMake Error' in the cmake.log file. 请问这是什么原因
我已经配置了pmemd24的source环境

Huschein

milk_q 发表于 2025-8-8 20:59
好的 谢谢您 我改了一下安装的最新的pmemd24+ambertools25按照官网的手册 在修改run_cmake里的-DOWNLOAD_ ...

你这也没把报错发出来啊 你自己看一下报错吧 大概率就是缺了什么python包 然后对应地装一下就好 amber自带的报错提示很容易理解 如果之前安装失败了 建议clean_cmake一下后再run_cmake