On Sun, Nov 1, 2015 at 1:34 PM, Martina Devi <martinadevi2011.gmail.com>
wrote:
> 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.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sun Nov 01 2015 - 11:00:04 PST
