Re: [AMBER] chamber problem

From: Jason Swails <>
Date: Tue, 19 Feb 2019 22:37:38 -0500

On Tue, Feb 19, 2019 at 11:33 AM Prabir Khatua <>

> 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.


Jason M. Swails
AMBER mailing list
Received on Tue Feb 19 2019 - 20:00:01 PST
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