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标题: 求助MCPB无法使用 [打印本页]

作者
Author: 八月的雨季 时间: 2020-5-12 20:43
标题: 求助MCPB无法使用
各位同仁，我使用MCPB构建金属位点的力场，输入：MCPB.py -i 4QHE.in -s 1，这一步应该会生成高斯计算电荷的输入文件，但是MCPB并没能调动起来，报了：Traceback (most recent call last): File "/home/wzx/Software/amber18/bin/MCPB.py", line 29, in <module> from pymsmt.mcpb.gene_model_files import get_ms_resnames, gene_model_files这个问题。我也上网查了很多资料，但大多也没说清楚这个问题出在哪个原因。还请各位不吝赐教，谢谢。

作者
Author: chenjinfeng850 时间: 2020-5-13 07:28
看起来像是你金属或者金属周围的残基命名的问题，跟着amber官网MCPB.py的教程仔细检查，根据教程的要求命名残基

作者
Author: CCCC 时间: 2020-5-13 11:16
你这个报错我遇到过，解决方法是在运行MCPB之前要先在根目录下source，我是这么做的，你试试~

作者
Author: 八月的雨季 时间: 2020-5-13 13:34

CCCC 发表于 2020-5-13 11:16
你这个报错我遇到过，解决方法是在运行MCPB之前要先在根目录下source，我是这么做的，你试试~

您好，我在根目录下source wzx//software2/amber18/bin/MCPB.py,出现了以下问题：
bash:
This is the MCPB.py program written by Pengfei Li in Merz Research Group
at Michigan State University.
It is written to assist the metal center modeling in mixed systems
(especially the protein system).
It is a re-written python program of MCPB in MTK++.
It optimize the workflow of the MCPB and has better supports of different
ions and force feilds.
It supports modeling of more than 80 ions from +1 to +8 oxidation states.
It supports a series of AMBER force fields (GAFF, ff94, ff99, ff99SB, ff03,
ff03.r1, ff10, ff12SB, ff14SB).

To cite the program please use:
** P. Li, K. M. Merz, JCIM, 2016, 56, 599-604.

The parameterization scheme is adapted from:
** M. B. Peters, Y. Yang, B. Wang, L. Fusti-Molnar, M. N. Weaver, K. M. Merz,
JCTC, 2010, 6, 2935-2947.

The Seminario method is from:
** J. M. Seminario, IJQC, 1996, 30, 1271-1277.
: command not found...
bash: from: command not found...
bash: from: command not found...
bash: from: command not found...
bash: from: command not found...
bash: wzx/software2/amber18/bin/MCPB.py: line 32: syntax error near unexpected token `('
bash: wzx/software2/amber18/bin/MCPB.py: line 32: `from pymsmt.mcpb.gene_final_frcmod_file import (gene_by_empirical_way,'

继续使用MCPB依然有问题
(base) [wzx@localhost home]$ MCPB.py
Traceback (most recent call last):
  File "/home/wzx/software2/amber18/bin/MCPB.py", line 29, in <module>
from pymsmt.mcpb.gene_model_files import get_ms_resnames, gene_model_files
  File "/home/wzx/software2/amber18/lib/python2.7/site-packages/pymsmt/mcpb/gene_model_files.py", line 7, in <module>
from pymsmt.mol.pdbio import get_atominfo_fpdb, writepdbatm
  File "/home/wzx/software2/amber18/lib/python2.7/site-packages/pymsmt/mol/pdbio.py", line 5, in <module>
from pymsmt.mol.mol import Atom, Residue, Molecule, get_reslist
  File "/home/wzx/software2/amber18/lib/python2.7/site-packages/pymsmt/mol/mol.py", line 2, in <module>
from pymsmt.mol.element import resnamel
  File "/home/wzx/software2/amber18/lib/python2.7/site-packages/pymsmt/mol/element.py", line 5, in <module>
from parmed.periodic_table import AtomicNum
  File "/home/wzx/software2/amber18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/__init__.py", line 22, in <module>
from parmed import unit, utils
  File "/home/wzx/software2/amber18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/unit/__init__.py", line 27, in <module>
from parmed.unit.unit import Unit, is_unit
  File "/home/wzx/software2/amber18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/unit/unit.py", line 35, in <module>
from parmed.utils.six import iterkeys
  File "/home/wzx/software2/amber18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/utils/__init__.py", line 3, in <module>
from parmed.utils.pairlist import find_atom_pairs
  File "/home/wzx/software2/amber18/lib/python2.7/site-packages/ParmEd-3.0.0+57.g74a84d30-py2.7-linux-x86_64.egg/parmed/utils/pairlist.py", line 5, in <module>
import numpy as np
ImportError: No module named numpy
(base) [wzx@localhost home]$

作者
Author: CCCC 时间: 2020-5-13 14:42

八月的雨季发表于 2020-5-13 13:34
您好，我在根目录下source wzx//software2/amber18/bin/MCPB.py,出现了以下问题：
bash:
This is the ...

不是…… 是直接source 即可 source ~/.cshrc 或者在根目录下source

作者
Author: 八月的雨季 时间: 2020-5-13 20:45

chenjinfeng850 发表于 2020-5-13 07:28
看起来像是你金属或者金属周围的残基命名的问题，跟着amber官网MCPB.py的教程仔细检查，根据教程的要求命名 ...

非常感谢您的回复，应该不是我输入文件的问题，换了一台机器很正常。

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