Dear Amber,
I want to delete bonds in my topology file and then run some analysis
using pytraj but can't figure out how to do it.
Can you help me?
See below
Thanks
Tom
This CPPTRAJ script works!
cpptraj sys.parm7
change removebonds :358.O3' :1.P
change removebonds :716.O3' :359.P
parmwrite out new.sys.parm7
quit
BUT trying to do something similar in pytraj does not work
nano 195% python3
Python 3.6.15 (default, Sep 23 2021, 15:41:43) [GCC] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> import pytraj as pt
>>> import pandas as pd
>>> import glob
>>> ######################
... top = pt.load_topology('sys.parm7')
>>> top
<Topology: 54271 atoms, 2664 residues, 18 mols, non-PBC>
>>> cpptrajtext = '''
... change removebonds :358.O3' :1.P
... change removebonds :716.O3' :359.P
... '''
>>> pt.io.load(cpptrajtext)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib64/python3.6/site-packages/pytraj/io.py", line 124, in load
traj = load_traj(filename, top, stride=stride)
File "/usr/lib64/python3.6/site-packages/pytraj/io.py", line 242, in
load_traj
top = load_topology(filename)
File "/usr/lib64/python3.6/site-packages/pytraj/io.py", line 527, in
load_topology
'n_atoms = 0: make sure to load correct Topology filename '
RuntimeError: n_atoms = 0: make sure to load correct Topology filename
or load supported topology (pdb, amber parm, psf, ...)
>>> parmedtext='''
... deleteBond :716.O3' :359.P
... deleteBond :358.O3' :1.P
... '''
>>> pt.io.load_parmed(parmedtext)
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/usr/lib64/python3.6/site-packages/pytraj/externals/load_other_packages.py",
line 22, in load_parmed
from parmed.amber import AmberParm
File "/usr/lib64/python3.6/site-packages/parmed/__init__.py", line 21,
in <module>
from . import unit, utils
File "/usr/lib64/python3.6/site-packages/parmed/utils/__init__.py",
line 4, in <module>
from ..topologyobjects import Atom
File "/usr/lib64/python3.6/site-packages/parmed/topologyobjects.py",
line 9, in <module>
from functools import cached_property
ImportError: cannot import name 'cached_property'
>>>
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Received on Mon Jul 10 2023 - 13:00:02 PDT
