AMBER Archive (2008)

Subject: Re: AMBER: changing pdb structure

From: Sasha Buzko (obuzko_at_ucla.edu)
Date: Thu Oct 09 2008 - 22:48:43 CDT

Taufik,
you can use Sirius (http://sirius.sdsc.edu) for basic amino acid
mutations via a simple replacement either through the structure or
sequence viewer. The side chain will be in some sort of a standard
conformation, but it shouldn't matter if you are going to run it
throught a minimization later on. The resulting structure can be saved
as pdb (or mol2). If you need the header, you can always manually add it
to the file.

Hope it helps

Sasha

taufik.alsarraj_at_utoronto.ca wrote:
> Hello,
> This is a general question.
>
> If i take a structure from the protein data bank, and the structure
> contains a protein and a DNA, is there a a software or a relatively
> simple method for modifying the protein sequence or the DNA sequence,
> e.g. changing an A to L (Protein) or changing a T to A (DNA). Short of
> manual modification in xleap or deleting the original DNA and creating
> a new one.
>
>
> Best,
> Taufik
>
>
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
> to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu