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标题: pdb4amber的环境变量该怎么设置呢？ [打印本页]

作者
Author: caroline 时间: 2020-6-19 16:34
标题: pdb4amber的环境变量该怎么设置呢？
请问ambertool20里pdb4amber的环境变量怎么设置呢？

作者
Author: chenjinfeng850 时间: 2020-6-19 17:43
只要正常安装好AmberTool20，设置好AMBERHOME就可以正常使用了

作者
Author: caroline 时间: 2020-6-19 19:38

chenjinfeng850 发表于 2020-6-19 17:43
只要正常安装好AmberTool20，设置好AMBERHOME就可以正常使用了

AMBERHOME已经设置好了，那我出现如下报错是为什么呢？
[YS_yangyf@ys0410 a]$ pdb4amber -i 1ema.pdb -o gfp.pdb --dry --reduce
Traceback (most recent call last):
  File "/home-ys/users/YS_yangyf/jly/Softwares/Amber/amber20/bin/pdb4amber", line 6, in <module>
from pkg_resources import load_entry_point
  File "/home-ys/users/YS_yangyf/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3253, in <module>
@_call_aside
  File "/home-ys/users/YS_yangyf/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3237, in _call_aside
f(*args, **kwargs)
  File "/home-ys/users/YS_yangyf/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 3266, in _initialize_master_working_set
working_set = WorkingSet._build_master()
  File "/home-ys/users/YS_yangyf/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 584, in _build_master
ws.require(__requires__)
  File "/home-ys/users/YS_yangyf/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 901, in require
needed = self.resolve(parse_requirements(requirements))
  File "/home-ys/users/YS_yangyf/anaconda3/lib/python3.7/site-packages/pkg_resources/__init__.py", line 787, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'pdb4amber==1.7.dev0' distribution was not found and is required by the application

作者
Author: chenjinfeng850 时间: 2020-6-19 20:55
看起来你是anaconda装的AmberTools？
那anaconda的lib有没有在环境变量里面？

看起来是conda的错误，你可以试一下用conda重装一下AmberTools

作者
Author: caroline 时间: 2020-6-19 21:13
本帖最后由 caroline 于 2020-6-19 21:19 编辑

chenjinfeng850 发表于 2020-6-19 20:55
看起来你是anaconda装的AmberTools？
那anaconda的lib有没有在环境变量里面？

对的，我是用anaconda安的，也将anaconda设置了环境变量。那我试一下用conda安装一下

作者
Author: 等等 时间: 2020-9-25 16:38
你好，请问你解决了这个问题了吗，我是安装的amber18，键入pdb4amber也出现你这样的结果，但我是用miniconda安装的
显示：Traceback (most recent call last):
  File "/home/bubble/amber18/bin/pdb4amber", line 6, in <module>
from pkg_resources import load_entry_point
  File "/home/bubble/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3241, in <module>
@_call_aside
  File "/home/bubble/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3225, in _call_aside
f(*args, **kwargs)
  File "/home/bubble/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 3254, in _initialize_master_working_set
working_set = WorkingSet._build_master()
  File "/home/bubble/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 583, in _build_master
ws.require(__requires__)
  File "/home/bubble/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 900, in require
needed = self.resolve(parse_requirements(requirements))
  File "/home/bubble/amber18/miniconda/lib/python2.7/site-packages/pkg_resources/__init__.py", line 786, in resolve
raise DistributionNotFound(req, requirers)
pkg_resources.DistributionNotFound: The 'pdb4amber==1.7.dev0' distribution was not found and is required by the application
想问问你是怎么解决的？

作者
Author: caroline 时间: 2020-9-29 16:38

等等发表于 2020-9-25 16:38
你好，请问你解决了这个问题了吗，我是安装的amber18，键入pdb4amber也出现你这样的结果，但我是用minicond ...

没有呢，我后来让工程师帮我安装的

作者
Author: boinboinxu 时间: 2023-9-21 17:38

caroline 发表于 2020-9-29 16:38
没有呢，我后来让工程师帮我安装的

请问去哪里找工程师哇？

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