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
>
>
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>
--
*Prabir Khatua*
*Postdoctoral Research Associate*
*Department of Chemistry & Biochemistry*
*University of Oklahoma*
*Norman, Oklahoma 73019*
*U. S. A.*
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Received on Wed Feb 13 2019 - 11:00:02 PST
