This is weird... Can you try re-compiling AmberTools in serial to see if
it fixes the issue? In particular, this looks like it's missing a required
ParmEd command that it uses to assign the appropriate radii.
HTH,
Jason
On Tue, Feb 23, 2016 at 10:39 AM, Elisa Pieri <elisa.pieri90.gmail.com>
wrote:
> Hi everybody,
>
> I have Amber14, but when I use the command
>
> cpinutil.py -p crys.solv10.parm7 -igb 2 -o crys.solv10.cpin -op
> crys.solv10.modO.parm7 -resnames AS4 GL4 HIP
>
> I get this error:
>
> /usr/lib/python2.7/dist-packages/numpy/oldnumeric/__init__.py:11:
> ModuleDeprecationWarning: The oldnumeric module will be dropped in Numpy
> 1.9
> warnings.warn(_msg, ModuleDeprecationWarning)
> Traceback (most recent call last):
> File "/home/elisa/amber14/bin/cpinutil.py", line 289, in <module>
> main(opt)
> File "/home/elisa/amber14/bin/cpinutil.py", line 256, in main
> changeradii(parm, 'mbondi2').execute()
> NameError: global name 'changeradii' is not defined
>
> and OC crys.solv10.modO.parm7 is not produced. What's happening?
>
> Elisa
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Feb 23 2016 - 19:00:05 PST
