Re: error - atom type not in psf

From: Vermaas, Joshua (
Date: Fri Sep 01 2017 - 11:36:19 CDT

Comment out the line with "!". It should be in the parameter file for the ions (grep ON1 *.prm).

On 09/01/2017 01:28 AM, Natasha Gupta wrote:
Thank you Josh - how do I correct this for NBFIX terms?

On Thursday, August 31, 2017, Vermaas, Joshua <<>> wrote:
Alright, upon further reflection, I hadn't considered potential NBFIX
terms for ions within the force field. If NAMD encounters an atomtype
within an NBFIX-specified interaction (such as those for ions with
carbonyls) that wasn't previously identified, this message will crop up
too. This is probably the 1% of time that I was unreasonably certain. :)


On 08/31/2017 10:29 AM, Vermaas, Joshua wrote:
> Hi Natasha,
> If NAMD is giving you that warning, I'm 99% sure that your psf file
> *does* contain ON1 somewhere. Load your psf file first, then your PDB,
> and search for "type ON1" within VMD. You'll find your atoms pretty
> quick (should be carbonyl oxygens within nucleic acids). You may have
> just not added in the nucleic acid parameters your system needs.
> -Josh
> On 08/31/2017 04:59 AM, Natasha Gupta wrote:
>>> Hi,
>>> I am trying to run minimization but am seeing the following error:
>>> My psf file does not have an atom type, "ON1". Has anyone seen this before? I would appreciate any suggestions.
>>> Regards,
>>> Natasha

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