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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Received on Tue Sep 24 2019 - 04:30:04 PDT
