From: Natasha Gupta (ngupta.r_at_gmail.com)
Date: Fri Sep 01 2017 - 02:28:46 CDT
Thank you Josh - how do I correct this for NBFIX terms?
On Thursday, August 31, 2017, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
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. :)
>
> -Josh
>
> 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:
> >>>
> >>> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE ON1
> >>>
> >>> 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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