I think the 3DNA code (
http://x3dna.org/) has scripts which will help you
do the mutations (for both DNA as well as RNA). It generates a pdb file for
the mutated sequence, and you can convert that to a format that leap
understands.
Debayan
On Sat, Mar 8, 2014 at 3:20 PM, Jason Swails <jason.swails.gmail.com> wrote:
> On Sat, Mar 8, 2014 at 2:14 AM, Raviprasad Aduri <
> aduri.goa.bits-pilani.ac.in> wrote:
>
> > Dear All,
> >
> > I am looking for some help on mutating residues in a RNA hairpin and then
> > energy minimizing the structure using AMBER. Given a PDB file, is it
> > possible to mutate a residue (say A to G) in AMBER and then carry out
> > energy minimization to see how that mutation effects the structure.
> >
>
> Amber has only very basic mutation capabilities. The tleap/xleap
> programs will automatically add atoms that are missing from any residues in
> the input PDB file. This is frequently used to fill in hydrogen atoms that
> are missing from X-ray crystallographic structures (whose resolution is too
> low to resolve hydrogen locations).
>
> This functionality can be leveraged to mutate structures, but it has some
> potentially severe drawbacks. If you change the residue name from A to G
> for a particular residue in your input PDB structure, leap will model that
> residue as a G instead of an A. In order to do this, though, you need to
> delete all atoms that are present only in an Adenine (since otherwise you
> will get complaints from tleap about unrecognized atoms in the residue).
> However, tleap is not very intelligent about where it adds missing atoms
> and simply adds them based on their positions in that residue's template.
>
> As a result, I suggest keeping as many atoms from the 'old' residue that
> are in the same location in the 'new' residue. You may have to rename some
> of the atoms to reflect their atom names in the new residue (names should
> follow the PDB standard). This approach minimizes the number of atoms that
> leap has to add, and will likely result in better starting structures.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Sat Mar 08 2014 - 08:30:02 PST
