How about this: create a small molecule in GaussView, that contains Na
atoms. Save as pdb, and compare the Na lines with the ones in your pdb
file. What differs?
Gustavo.
Em 01/11/2015 15:34, "Martina Devi" <martinadevi2011.gmail.com> escreveu:
> Thank you Sir Robert and Sir Gustavo for the suggestion.I very much
> appreciate the help.
>
> I gave the commands as given below:
>
> loadAmberParams frcmod.ionsjc_tip3p
>
> addions sample Na+ 0
>
> and save the pdb file.Yes, I can see the normal pdb contents. The sample
> pdb file is here. Please see and give your suggestion.
>
> I tried to replace the first "+" sign in the Na+ lines by a space but it
> didn't worked.
>
>
> Martina
>
> On Sun, Nov 1, 2015 at 10:34 PM, Gustavo Seabra <gustavo.seabra.gmail.com>
> wrote:
>
> > 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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Received on Sun Nov 01 2015 - 15:00:04 PST
