Just after doing source amber.sh we ran 'parmed AH_ff14SB_CMAP.prmtop' and
got
No module named 'simtk'
No module named 'numpy'
Thanks for your help.
Sunita
On Tue, Sep 24, 2019 at 5:13 PM Elvis Martis <elvis_bcp.elvismartis.in>
wrote:
> 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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Received on Tue Sep 24 2019 - 05:00:03 PDT
