Re: [AMBER] ions cannot be viewed in gaussview

From: Aleksandra Skoric <>
Date: Mon, 2 Nov 2015 14:54:44 +0100

Dear Martina,

How did you generate your pdb file?
I've just checked my pdb file (generated after the md run) and my Na+ ions
look perfectly fine. :)

But, I did notice that gview sometimes has a problem with atom recognition
no matter of columns 77-78.

In that case open the pdb structure, then open Atom list (Edit/Atom List),
and in Atom List Editor scroll down to find an atom that is not recognized
and then in Symbol column replace unrecognised atom with appropriate atom
(in your case N to Na). And then save modified structure and open again
with gview. That's all.


On Mon, Nov 2, 2015 at 2:41 PM, Jason Swails <> wrote:

> On Mon, Nov 2, 2015 at 12:44 AM, MOHD HOMAIDUR RAHMAN <
> >
> 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.
> >
> ‚Äčtleap does not print anything in the element field (ParmEd and cpptraj I
> think both *do* put something here, but I'm not positive about that).
> Which means if the original PDB came from tleap, then the elements must
> have been added "by hand" after-the-fact.
> All the best,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Mon Nov 02 2015 - 06:00:12 PST
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