I can open your file normally in Chimera. VMD also doesn't recognize the
Na+ ions, and I don't have access to GaussView now.
One suggestion: try to replace the first "+" sign in the Na+ lines by a
space. This worked for VMD and it recognized the pdb file after this
change. I believe this should solve the problem for GaussView as well.
Gustavo.
Em 01/11/2015 12:13, "Martina Devi" <martinadevi2011.gmail.com> escreveu:
> Can anybody rectify or give suggestion.
>
> Martina
>
>
> On Sun, Nov 1, 2015 at 12:42 AM, Martina Devi <martinadevi2011.gmail.com>
> wrote:
>
> > 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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> >> >>
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> >>
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> >
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Received on Sun Nov 01 2015 - 09:30:04 PST
