Hi Jason,
Thank you for your reply. First, I loaded parmed interpreter by typing
parmed that opened parmed editor. Then, I used the
following command to generate prmtop file from the command prompt of parmed.
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 seems that very last line of the error i.e., "Action chamber failed
DuplicateParm: Willbold_IRF_1-42_6X2.psf already in ParmList" appears
if I use similar
command at least twice from the same parmed editor command prompt. Thus, it
seems that psf file gets
saved once it has been used on the command prompt. However, I am wondering
whether the warning message that is being
printed i.e., "ParameterWarning: ('CC', 'OC', 'X', 'X') and ('CC', 'CT1',
'X', 'X') match improper ('CC', 'CT1', 'OC', 'OC'). Using ('CC', 'OC', 'X',
'X')" can be
ignored of care should be taken. Please note that these warning messages
are being printed irrespective of number of times I typed the above
command.
I am getting one more warning on the very first attempt (not 2nd or 3rd) of
such command , as follows
UserWarning: WARNING: Ignoring "DELETE ACCE NE2" because entity type ACCE
not used.
I hope it should not matter whether I provide the psf file in charmm or
x-plor format, as Amber 18 recognizes the format and does the conversion
accordingly. I am providing the psf file in x-plor format. Please let me
know if the problem is arising due to x-plor format. I hope I provided the
details the commands that I used.
Thanks,
Prabir
On Tue, Feb 19, 2019 at 2:03 AM Jason Swails <jason.swails.gmail.com> wrote:
> 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.*
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Jason M. Swails
> _______________________________________________
> 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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Received on Tue Feb 19 2019 - 09:00:03 PST
