This the sample pdb with the Na ion. Is the format of pdb file correct?
Thanks in advance
Martina
On Sat, Oct 31, 2015 at 11:23 PM, Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:
> Any chance you could send us a sample PDB file which illustrates the
> problem?
>
> Gustavo Seabra
>
>
>
> > Em 31/10/2015, à(s) 13:08, Martina Devi <martinadevi2011.gmail.com>
> escreveu:
> >
> > 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 - 12:30:03 PDT
