Thank you Jason. Hopefully, it should work fine.
Prabir
On Tue, Feb 19, 2019 at 9:38 PM Jason Swails <jason.swails.gmail.com> wrote:
> On Tue, Feb 19, 2019 at 11:33 AM Prabir Khatua <prabir07chem.gmail.com>
> wrote:
>
> > 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.
>
>
> Each time you use the 'chamber' action in ParmEd, it saves the parm under
> the name of the PSF file. So if you use the same command twice, it'll try
> to save a parm under the same name. To avoid silently overwriting things,
> ParmEd doesn't permit two parms to have the same name.
>
> > 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
>
>
> Yes, this is probably more informational than warning.
>
> > 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.
> >
>
> This is safely ignored.
>
>
> > I hope it should not matter whether I provide the psf file in charmm or
> > x-plor format,
>
>
> Both formats should work fine.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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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 20 2019 - 08:30:02 PST
