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
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Received on Fri Oct 30 2015 - 09:00:05 PDT
