Sidetopic : How do you create a primary structure ?

Discussions on how to set up simulations, typically starting from a pdb file.
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m.kalavera
Posts: 29
Joined: Mon Feb 09, 2009 10:58 am

Sidetopic : How do you create a primary structure ?

Post by m.kalavera » Thu May 21, 2009 9:18 am

Hello everyone,
this is not really an direct question about the simulation setup, but it is connected to in this context.
How do you create an simple primary structure of an protein ? Which tools do you use ?
I have done some mutations for my protein (secondary structure) with the help of modeller and I used some peptidebuilder in the internet, which revealed as unfeasible.
Is there any commen tool or method to create a simpel, non folded primary strand by only the sequnece given ?

Thx for your support and ideas,
your M.Kalavera

martin
Developer
Posts: 38
Joined: Sun Jun 15, 2008 10:27 pm

Re: Sidetopic : How do you create a primary structure ?

Post by martin » Fri May 22, 2009 9:07 am

Hi,

Look that the minimizer_cyclical_sequence test job. You can load from sequence. Default is extended structure, but you can also set it helical in the input file. Note the use of 3 and 1 letter side chain identifiers. That is to allow setting the charged state of ionizable residues: e.g. LYS = charged, LYN = neutral lysine (c.f. forcefield and database files).
Hope this helps!
Best wishes,
Martin

m.kalavera
Posts: 29
Joined: Mon Feb 09, 2009 10:58 am

Re: Sidetopic : How do you create a primary structure ?

Post by m.kalavera » Tue May 26, 2009 9:50 am

Is it possible to apply any patches on the terminal residues ?

Greets ,M.kalavera

martin
Developer
Posts: 38
Joined: Sun Jun 15, 2008 10:27 pm

Re: Sidetopic : How do you create a primary structure ?

Post by martin » Tue May 26, 2009 10:10 am

Hi,

ACE (acetylate) and AME (amidate) are standard, just add to your sequence:
e.g.
ACE (LALA) AME

Best wishes,
martin

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