I can see ions in Gaussview just fine if I have a correctly loaded PDB and I do addions command followed by saving the PDB. What are your precise commands given? Can you see the normal PDB contents?
Dr. Robert Molt Jr.
r.molt.chemical.physics.gmail.com
Nigel Richards Research Group
Department of Chemistry & Chemical Biology
Indiana University-Purdue University Indianapolis
LD 326
402 N. Blackford St.
Indianapolis, IN 46202
> On Nov 1, 2015, at 10:12 AM, Martina Devi <martinadevi2011.gmail.com> wrote:
>
> Can anybody rectify or give suggestion.
>
> Martina
>
>
> On Sun, Nov 1, 2015 at 12:42 AM, Martina Devi <martinadevi2011.gmail.com>
> wrote:
>
>> This the sample pdb with the Na ion. Is the format of pdb file correct?
>>
>> Thanks in advance
>> Martina
>>
>> On Sat, Oct 31, 2015 at 11:23 PM, Gustavo Seabra <gustavo.seabra.gmail.com
>>> wrote:
>>
>>> 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 Sun Nov 01 2015 - 07:30:04 PST
