Just source the $AMNERHOME/amber.sh before typing parmed.
Best Regards
On Tue, 24 Sep 2019 at 16:58, Sunita Patel <sunita.patel.cbs.ac.in> wrote:
> Dear Elvis,
>
> When we checked 'parmed AH_leap_struct_CMAP.prmtop' following errors
> appeared.
>
> ModuleNotFoundError: No module named 'simtk'
> ModuleNotFoundError: No module named 'numpy'
>
> Looks like some of the modules are missing in my Amber18.
> Pls suggest how to rectify it.
>
> Thanks for your help.
>
> Sincerely,
> Sunita
>
>
>
> On Thu, Sep 19, 2019 at 5:12 PM Elvis Martis <elvis_bcp.elvismartis.in>
> wrote:
>
> > hello
> > you would want to check the validity of the new prmtop file after adding
> > CMAP parameters using parmed,
> > See the following commands
> > source $AMBERHOME/amber.sh
> > parmed AH_leap_struct_CMAP.prmtop
> > checkValidity
> >
> > If the prmtop file is corrupted while adding CMAP parameters parmed will
> > tell.
> >
> > Best Regards
> >
> >
> >
> > On Thu, 19 Sep 2019 at 17:01, Sunita Patel <sunita.patel.cbs.ac.in>
> wrote:
> >
> > > Dear Users,
> > >
> > > We are trying to convert *.prmtop and *.rst files obtained after energy
> > > minimization into a pdb file using ambpdb command. The *.prmtop file is
> > > obtained by adding extra CMAP parameters (FF14IDPSFF) to the original
> > > prmtop file obtained from FF14SB force field. However, we got the
> > following
> > > error message.
> > >
> > > ambpdb -p AH_leap_struct_CMAP.prmtop -c AH_struct_min.rst >
> > > AH_struct_min.pdb
> > > Segmentation fault (core dumped)
> > >
> > > When we are converting the prmtop file to pdb without adding CMAP
> > > parameters, we could successfully do that without any error.
> > > How can we get the pdb file by using the prmtop file with the CMAP
> > > parameters?
> > >
> > > Sincerely,
> > > Sunita
> > > _______________________________________________
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> > >
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> >
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Received on Tue Sep 24 2019 - 05:00:02 PDT
