Any chance you could send us a sample PDB file which illustrates the problem?
Gustavo Seabra
> Em 31/10/2015, à(s) 13:08, Martina Devi <martinadevi2011.gmail.com> escreveu:
>
> Yes it is a pdb file. I replaced the Na+ with NA also but it didn't
> work.Now I can view the Nitrogen atom instead of the Sodium atom. So the
> viewing program can't read the Na atom as it is recognizing only the N
> atom? Can these be the reason?
>
> Thank you
> Martina
>
> On Fri, Oct 30, 2015 at 9:20 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
>> 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 Sat Oct 31 2015 - 11:00:03 PDT
