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标题: 求助：mmpbsa计算时报错没有'alamdcrd'模块 [打印本页]

作者
Author: Cuie 时间: 2023-4-21 20:37
标题: 求助：mmpbsa计算时报错没有'alamdcrd'模块
大家好，
我用amber mmgbsa测试计算蛋白-配体结合自由能时，在运行过程中提示如下错误：
$AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -do FINAL_DECOMP_MMPBSA.dat -sp complex_solv.prmtop -cp complex.prmtop -rp receptor.prmtop -lp ligand.prmtop -y prod1.mdcrd > progress.log

  File "/media/c/UN1/amber20/bin/MMPBSA.py", line 4, in <module>
__import__('pkg_resources').run_script('MMPBSA.py==16.0', 'MMPBSA.py')
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 667, in run_script
self.require(requires)[0].run_script(script_name, ns)
  File "/usr/lib/python3/dist-packages/pkg_resources/__init__.py", line 1470, in run_script
exec(script_code, namespace, namespace)
  File "/media/c/UN1/amber20/lib/python3.8/site-packages/./MMPBSA.py-16.0-py3.8.egg/EGG-INFO/scripts/MMPBSA.py", line 99, in <module>
  File "/media/c/UN1/amber20/lib/python3.8/site-packages/./MMPBSA.py-16.0-py3.8.egg/MMPBSA_mods/main.py", line 167, in file_setup
self.mut_str, mutant_residue = make_mutant_trajectories(INPUT, FILES,
  File "/media/c/UN1/amber20/lib/python3.8/site-packages/./MMPBSA.py-16.0-py3.8.egg/MMPBSA_mods/make_trajs.py", line 298, in make_mutant_trajectories
from alamdcrd import MutantMdcrd, GlyMutantMdcrd
ModuleNotFoundError: No module named 'alamdcrd'

Fatal Error!
All files have been retained for your error investigation:
You should begin by examining the output files of the first failed calculation.
Consult the "Temporary Files" subsection of the MMPBSA.py chapter in the
manual for file naming conventions.

我也在网上和amber手册上搜索了这个alamdcrd，但是没找到相关信息。
各位老师是否遇到过类似问题，有什么头绪吗？

我的mmpbas.in如下
&general
startframe=50, endframe=2000, interval=50,
keep_files=0, debug_printlevel=2
/
&gb
igb=2, saltcon=0.1
/
&pb
istrng=0.100,
/

作者
Author: rpestana94 时间: 2023-4-21 22:07
本帖最后由 rpestana94 于 2023-4-21 09:08 编辑

Looks like maybe something went wrong in AmberTools instalation, when it install minicuda, try installing again AmberTools

作者
Author: Cuie 时间: 2023-4-22 10:18

rpestana94 发表于 2023-4-21 22:07
Looks like maybe something went wrong in AmberTools instalation, when it install minicuda, try insta ...

Thank you for your suggestion.

I'll try it out using the AmberTools22 installed by miniconda.

作者
Author: Cuie 时间: 2023-4-22 20:47

rpestana94 发表于 2023-4-21 22:07
Looks like maybe something went wrong in AmberTools instalation, when it install minicuda, try insta ...

The AmberTools installed using Miniconda can perform mmpbsa calculations normally. The reason for the above errors is estimated to be that some parts of Amber were not properly configured during installation. Thank you again

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