Thank you Mohd Homaidur Rahman
I understand now that the elemental information in the pdb file is at place
78-79 so it is reading along N as nitrogen instead of Na. But this the pdb
file which is generated after the run. So did any other AMBER users
experienced this process?
Martina
On Sun, Nov 1, 2015 at 9:44 PM, MOHD HOMAIDUR RAHMAN <rahmanhpu.gmail.com>
wrote:
> 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
> > > > > >> >> _______________________________________________
> > > > > >> >> AMBER mailing list
> > > > > >> >> AMBER.ambermd.org
> > > > > >> >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >> >>
> > > > > >> > _______________________________________________
> > > > > >> > AMBER mailing list
> > > > > >> > AMBER.ambermd.org
> > > > > >> > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >>
> > > > > >>
> > > > > >> _______________________________________________
> > > > > >> AMBER mailing list
> > > > > >> AMBER.ambermd.org
> > > > > >> http://lists.ambermd.org/mailman/listinfo/amber
> > > > > >>
> > > > > >
> > > > > >
> > > > > _______________________________________________
> > > > > AMBER mailing list
> > > > > AMBER.ambermd.org
> > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > >
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Nov 02 2015 - 05:30:06 PST
