IOError on netCharge indicates parmEd evidently expects a filename in
the place you are putting the netCharge cmd.
Bill
On 8/2/20 4:40 PM, Billiot, Eugene wrote:
> 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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
Phobrain.com
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Aug 02 2020 - 18:00:03 PDT
