Hello Folks,
I am trying to calculate the overall net charge of a from the prmtop file to help determine if the charges are correct. The the Amber 18 manual in section 14.2.2.34 it states the following :
14.2.2.34. netCharge
Usage: netCharge [mask]
This command will calculate the net charge of all atoms belonging to a specific mask. If no mask is provided, it
returns the net charge of all atoms in the topology file.
When I try to run what I think is the correct command "parmed netCharge -p ULV_mic.prmtop" , I get the error shown below of "IOError: netCharge does not exist". Can somine please tell me what I am doing wrong.
[ebill.cs-127a-26042 ULV_07302020_restraint_study]$ parmed netCharge -p ULV_mic.prmtop
. . . . . . . . . + .
. . : . .. :. .___---------___.
. . . . :.:. _".^ .^ ^. '.. :"-_. .
. : . . .:../: . .^ :.:\.
. . :: +. :.:/: . . . . . .:\
. : . . _ :::/: . ^ . . .:\
.. . . . - : :.:./. . .:\
. . . :..|: . . ^. .:|
. . : : ..|| . . . !:|
. . . . ::. ::\( . :)/
. . : . : .:.|. ###### .#######::|
:.. . :- : .: ::|.####### ..########:|
. . . .. . .. :\ ######## :######## :/
. .+ :: : -.:\ ######## . ########.:/
. .+ . . . . :.:\. ####### #######..:/
:: . . . . ::.:..:.\ . . ..:/
. . . .. : -::::.\. | | . .:/
. : . . .-:.":.::.\ ..:/ .~~~~~~~~~~~.
. -. . . . .: .:::.:.\. .:/,: Prepare to \
. . . : : ....::_:..:\ ___. :/ . be |
. . . .:. .. . .: :.:.:\ :/ \ P A R M E D |
+ . . : . ::. :.:. .:.|\ .:/| \~~~~~~~~~~~'
. + . . ...:: ..| --.:|
. . . . . . . ... :..:.."( ..)"
. . . : . .: ::/ . .::\
ParmEd: a Parameter file Editor
Loaded Amber topology file ULV_mic.prmtop
Traceback (most recent call last):
File "/home/ebill/amber18/bin/parmed", line 11, in <module>
load_entry_point('ParmEd==3.2.0', 'console_scripts', 'parmed')()
File "/home/ebill/amber18/lib/python2.7/site-packages/ParmEd-3.2.0-py2.7-linux-x86_64.egg/parmed/scripts.py", line 128, in clapp
amber_prmtop.add_parm(parm)
File "/home/ebill/amber18/lib/python2.7/site-packages/ParmEd-3.2.0-py2.7-linux-x86_64.egg/parmed/tools/parmlist.py", line 39, in add_parm
parm = load_file(name, structure=True)
File "/home/ebill/amber18/lib/python2.7/site-packages/ParmEd-3.2.0-py2.7-linux-x86_64.egg/parmed/formats/registry.py", line 168, in load_file
raise IOError('%s does not exist' % filename)
IOError: netCharge does not exist
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Received on Sun Aug 02 2020 - 17:00:03 PDT
