I didn't realise it was part of amber, however I've encountered this issue when I type parmed in the command line:
Traceback (most recent call last):
File "/home/swalsworth/amber20_src/bin/parmed", line 33, in <module>
sys.exit(load_entry_point('ParmEd===at20RC5-54.g5702a232fe.dirty', 'console_scripts', 'parmed')())
File "/home/swalsworth/amber20_src/bin/parmed", line 22, in importlib_load_entry_point
for entry_point in distribution(dist_name).entry_points
File "/home/swalsworth/amber20_src/miniconda/lib/python3.8/importlib/metadata.py", line 504, in distribution
return Distribution.from_name(distribution_name)
File "/home/swalsworth/amber20_src/miniconda/lib/python3.8/importlib/metadata.py", line 177, in from_name
raise PackageNotFoundError(name)
importlib.metadata.PackageNotFoundError: ParmEd
I'm aware that I might need to edit my pythonpath. If so, do you know where to find the appropriate package?
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: 03 February 2022 11:50
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] Modifying prmtop/inpcrd files
On Thu, Feb 03, 2022, Sam Walsworth (Researcher) wrote:
>>I think what you might want is parmed- you can add dihedrals by
>>addDihedral, and I think you can add bonds/angles by setBond and
>>setAngle? It's been a while since I've done it, but an example for an extra
>>dihedral could be like
>>
>>addDihedral :9.N1 :1.C6 :1.C5 :1.C4 0.0 2.0 1.2
>Yes, this looks like it could be the solution. Do you have any
>guides/walkthroughs of how to use it? I've tried to go through the github
>but found myself getting confused with exactly how to load it correctly and
>correct syntax etc.
Can you say what you tried, and what didn't work? You don't need github:
the parmed program is a part of AmberTools. Type "parmed" on the command
line, then "help" at the prompt, followed by "help <command>" for help on
specific commands. Section 15.2 in the Manual has more detailed
explanations, and section 15.2.3 has a number of commented examples. I hope
these will help.
....dac
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Received on Thu Feb 03 2022 - 08:30:02 PST
