Re: [AMBER] ions cannot be viewed in gaussview

From: Jason Swails <>
Date: Mon, 2 Nov 2015 08:41:43 -0500

On Mon, Nov 2, 2015 at 12:44 AM, MOHD HOMAIDUR RAHMAN <>

> 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 M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 02 2015 - 06:00:05 PST
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