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 - 07:30:02 PST
