Yes it is a pdb file. I replaced the Na+ with NA also but it didn't
work.Now I can view the Nitrogen atom instead of the Sodium atom. So the
viewing program can't read the Na atom as it is recognizing only the N
atom? Can these be the reason?
Thank you
Martina
On Fri, Oct 30, 2015 at 9:20 PM, Jason Swails <jason.swails.gmail.com>
wrote:
> On Fri, Oct 30, 2015 at 10:18 AM, Martina Devi <martinadevi2011.gmail.com>
> wrote:
>
> > Dear Amber users
> >
> > I used the loadAmberParams frcmod.ionsjc_tip3p command to place the Na
> ions
> > around the system.
> >
> > loadAmberParams frcmod.ionsjc_tip3p
> >
> > addions sample Na+ 0
> >
>
> Try replacing Na+ with NA.
>
>
> >
> > Though the parameter and coordinates file are generated and contain the
> > ions, the Na ions cannot be viewed in gaussview. So am I missing any step
> > that the Na ions cannot be viewed. Any suggestion will be of help.
> >
>
> I'm not sure why Gaussview would struggle with the Na+ atoms. Are you
> feeding Gaussview a PDB file? How did you make whatever file you're
> feeding to Gaussview?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sat Oct 31 2015 - 09:30:03 PDT
