Hi all :)
Recently I've been needed to parametrise my short protein mollecule by ATB
server for futher MD simulation.
The input pdb file for that server must consist of CONNECT records at the
bottom of such pdb.
How I could add such missing CONNECT records for my pdb ?
I've tried
set connect_mode, 1
but saved pdb still have not contained CONNECT :(
Thanks for help
James
30 марта 2012 г. 13:52 пользователь James Starlight
<jmsstarli...@gmail.com>написал:
> Hi all :)
>
>
> Recently I've been needed to parametrise my short protein mollecule by ATB
> server for futher MD simulation.
>
> The input pdb file for that server must consist of CONNECT records at the
> bottom of such pdb.
>
> How I could add such missing CONNECT records for my pdb ?
>
> I've tried
>
> set connect_mode, 1
>
>
>
> but saved pdb still have not contained CONNECT :(
>
> Thanks for help
>
> James
>
> 21 марта 2012 г. 13:14 пользователь Tsjerk Wassenaar
> <tsje...@gmail.com>написал:
>
> Hi James,
>>
>> Pymol adds a TER statement at the end of each continuous piece of the
>> protein.
>>
>> Cheers,
>>
>> Tsjerk
>>
>> 2012/3/21 James Starlight <jmsstarli...@gmail.com>:
>> > Hi Tsjerk,
>> >
>> > I'm not quite understood if pymol adds TER enty after residues wich
>> consist
>> > of missing atoms or in the place with the missing residues ( e.g in
>> loops
>> > of GPCRs or other flexible regions) ?
>> >
>> > James
>> >
>> > 21 марта 2012 г. 10:38 пользователь Tsjerk Wassenaar <tsje...@gmail.com
>> >
>> > написал:
>> >
>> >> Hi James,
>> >>
>> >> Broken refers to non-continuity of a chain, i.e. missing residues.
>> Broken
>> >> does not mean wrong... But for the rest, I admitted to be wrong with my
>> >> arguments already :p
>> >>
>> >> Cheers,
>> >>
>> >> Tsjerk
>> >>
>> >> On Mar 21, 2012 6:47 AM, "James Starlight" <jmsstarli...@gmail.com>
>> wrote:
>> >>
>> >> Hi Tsjerk!
>> >>
>> >> It's very strange because I've obtained all same structures with the
>> same
>> >> TER statements in the body of the pdb file in the case of processing of
>> >> x-ray structures of GPCRs ( It's different membrane proteins solved by
>> the
>> >> different lab groups in the different time ). So it's strange that all
>> of
>> >> those structures were broken!
>> >>
>> >> James
>> >>
>> >> 20 марта 2012 г. 14:35 пользователь Tsjerk Wassenaar <
>> tsje...@gmail.com>
>> >> написал:
>> >>
>> >> > > Hi James, > > In addition to Thomas' answer... What is _wrong_
>> about
>> >> > > the TER > statement? Your ...
>> >>
>> >>
>> >
>>
>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>>
>> post-doctoral researcher
>> Molecular Dynamics Group
>> * Groningen Institute for Biomolecular Research and Biotechnology
>> * Zernike Institute for Advanced Materials
>> University of Groningen
>> The Netherlands
>>
>
>
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