In your case I check the pdb every thing fine except elemental information.
In standard pdb file elemental information occupied at place 77-78. while
in your pdb file it is at place 78-79. That why Gauss View reading as "N"
Now my question to Jason why element information printing in non-standard
pdb format or this is Martina editing mistake.
Thanks & regards
Rahman
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
*Md Homaidur Rahman*
PhD Research Scholar
Computational Biophysics Lab.
Department of Biotechnology
Indian Institute of Technology-Madras
Chennai-600 036
*Mobile No = +91- 7845991785*
'''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''''
On Mon, Nov 2, 2015 at 4:07 AM, Gustavo Seabra <gustavo.seabra.gmail.com>
wrote:
> 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 - 22:00:03 PST
