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 - 07:30:03 PST
