AMBER Archive (2008)

Subject: RE: AMBER: changing pdb structure

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Thu Oct 09 2008 - 22:29:24 CDT

Hi Taufik,

I don't know if there is a specific program that can do this, however, one
simple thing you can try is to edit the pdb and go to the residue you want
to change. Delete all the atoms from this residue except the backbone atoms
(and perhaps keep CB as well). Then change the name of the residue to the
new residue you want and load it into leap. Leap will then add all of the
missing atoms for this new residue.

Note, this will of course leave you with steric clashes so you may want to
relax the structure carefully by minimizing and then running MD with
restraints on the modified residue etc.

Good luck,
Ross

> -----Original Message-----
> From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> Of taufik.alsarraj_at_utoronto.ca
> Sent: Thursday, October 09, 2008 7:35 PM
> To: amber_at_scripps.edu
> Subject: AMBER: changing pdb structure
>
> 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
>
>
>
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