Best Regards
On Tue, 24 Sep 2019 at 17:21, Sunita Patel <sunita.patel.cbs.ac.in> wrote:
> Just after doing source amber.sh we ran 'parmed AH_ff14SB_CMAP.prmtop' and
> got
> No module named 'simtk'
> No module named 'numpy'
> Just install it using
amber.conda install -c anaconda numpy >> this should solve the missing numpy
amber.conda install -c omnia openmm >> this should solve the missing simtk
problem
Hope this helps.
> 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 - 05:00:04 PDT
