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 <jmsstarlight@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 <tsjerkw@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 <jmsstarlight@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 <tsjerkw@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" <jmsstarlight@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 <tsjerkw@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