[AMBER] how to calculate net charge of "molecule" using the command "netCharge"

From: Billiot, Eugene <Eugene.Billiot.tamucc.edu>
Date: Sun, 2 Aug 2020 23:40:27 +0000

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
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