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 - 11:00:03 PST
