Re: [AMBER] ions cannot be viewed in gaussview

From: Jason Swails <>
Date: Sun, 1 Nov 2015 13:43:48 -0500

On Sun, Nov 1, 2015 at 1:34 PM, Martina Devi <>

> 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.

Try adding the element information to the PDB file. This is done by adding
the letters NA to columns 77 and 78 of the PDB file (for sodium).

This is *probably* how Gaussian determines element information.

If that still doesn't work, ask Gaussian.


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sun Nov 01 2015 - 11:00:04 PST
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