The error states that the same topology has been loaded twice. There are a
couple ways that could have happened, but without seeing the full set of
commands (including the parmed command you used to start the program), I
can't point out where that happened.
HTH,
Jason
On Wed, Feb 13, 2019 at 1:31 PM Prabir Khatua <prabir07chem.gmail.com>
wrote:
> Dear Sir,
>
> Thank you so much for your reply and suggestion. It's working after I typed
> 'source amber.sh'. Now, I am using chamber command
> under parmed interpreter using the following
>
> chamber -top top_all36_prot.rtf -param par_all36m_prot.prm -psf
> Willbold_IRF_1-42_6X2.psf -crd Willbold_IRF_1-42_6X2.pdb
>
> It is now working now. However, I am receiving some chamber failure with
> some warning which is attached herewith the mail.
> Please help me to fix this issue or let me know if it is fine to move
> forward.
>
> Thank you,
>
> Sincerely,
>
> Prabir
>
>
> On Wed, Feb 13, 2019 at 4:05 AM David Case <david.case.rutgers.edu> wrote:
>
> > On Wed, Feb 13, 2019, Prabir Khatua wrote:
> > >
> > >Thank you for your reply. I assume the executable to be parmed that will
> > >job similar job as that of chamber. As per your suggestion,
> > >I have installed AmberTools18 to do this conversion. I am using the
> > >following command
> > >
> > >$AMBERHOME/bin/parmed -top top_all36_prot.rtf -param par_all36m_prot.prm
> > >-cmap -xpsf Willbold_IRF_1-42_6X2.psf -crd -p prot.prmtop -inpcrd
> > >prot.inpcrd
> >
> > Above is not correct; you can consult the section on ParmEd in the
> > Reference Manual (Section 14.2), or just type "help" at the parmed
> prompt.
> >
> > > raise DistributionNotFound(req, requirers)
> > >pkg_resources.DistributionNotFound: The 'ParmEd==3.0.0+57.g74a84d30'
> > >distribution was not found and is required by the application
> >
> > Not sure about this error: be sure you have typed "source amber.sh" in
> > the AMBERHOME directory, so that your environment is properly set up.
> >
> > ...good luck....dac
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
>
> *Prabir Khatua*
> *Postdoctoral Research Associate*
> *Department of Chemistry & Biochemistry*
> *University of Oklahoma*
> *Norman, Oklahoma 73019*
> *U. S. A.*
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
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Received on Mon Feb 18 2019 - 13:00:02 PST
