I think the message is a bit misleading,
(we met similiar issue in the topic: "[AMBER] Could not import Amber Python
modules when using mdout_analyzer.py")
You can try
1. amber.python $AMBERHOME/bin/cpinutil.py ...
2. if that does not help,
try
amber.python -c "from parmed.amber import titratable_residues as residues;
print(residues)"
to see if you are able to import parmed or not.
Hai
On Thu, Sep 21, 2017 at 4:56 PM, Pacheco, Sayuri <
sayuri.pacheco.987.my.csun.edu> wrote:
> Yes This problem started after we updated to AmberTools17 (with full
> recompile).
>
> The /usr/local/amber16/amber.sh is being sourced and echo $AMBERHOME shows
> that $AMBERHOME is defined. However, within the python script of
> cpinutil.py it appears (from the error) that it is unable to find
> $AMBERHOME.
>
> cpinutil.py was working before the update, and we updated to AmberTools17
> to be able to use the new –op option.
>
>
>
> On Sep 21, 2017 1:24 PM, "Adrian Roitberg" <roitberg.ufl.edu> wrote:
>
> > Did you do this: ?
> >
> > Please make sure you
> > have sourced /usr/local/amber16/amber.sh (if you are using
> sh/ksh/bash/zsh)
> > or /usr/local/amber16/amber.csh (if you are using csh/tcsh)
> >
> >
> > adrian
> >
> >
> > On 9/21/17 3:45 PM, Pacheco, Sayuri wrote:
> > > Hello,
> > > I'm trying to run a constant pH MD simulation in explicit solvent and
> in
> > > order to prepare a modified prmtop file, the amber17 says to use a
> python
> > > script. The python script is $cpinutil.py -igb 2 -resnames AS4 GL4 -p
> > > <tleap_prmtop> \ -op <new_radii.prmtop>. This is the error that I'm
> > getting.
> > >
> > > cpinutil.py -igb 2 -resnames AS4 GL4 -p tassmod4_pH7.prmtop -op
> > > raddi_tassmod4_pH7.prmtop
> > >
> > > Traceback (most recent call last):
> > >
> > > File "/usr/local/amber16/bin/cpinutil.py", line 24, in <module>
> > >
> > > (amberhome, amberhome))
> > >
> > > ImportError: Could not import Amber Python modules. Please make sure
> you
> > > have sourced /usr/local/amber16/amber.sh (if you are using
> > sh/ksh/bash/zsh)
> > > or /usr/local/amber16/amber.csh (if you are using csh/tcsh)
> > >
> > >
> > > Thank you,
> > >
> > > Sayuri
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > --
> > Dr. Adrian E. Roitberg
> > University of Florida Research Foundation Professor
> > Department of Chemistry
> > University of Florida
> > roitberg.ufl.edu
> > 352-392-6972
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Thu Sep 21 2017 - 22:00:02 PDT
