Dear Jonathan,
You could edit the PDB file: (i) remove the side chain of the amino
acid to be mutated; (ii) rename the backbone of this residue according
to the residue name of the mutation. Then, you load the modified PDB
file in the LEAP program, which will automatically add the missing
atoms (i.e. the side chain) in agreement with the FF library of the
mutated residue.
regards, Francois
> The basic (or complex) question I have is:
>
> How do you take a PDB and change one residue to another residue?
> (essentially a point mutation of an existing structure)
>
> I thought I remembered reading how it could be done, but looking back I
> can't seem to find where it might be. I can think of a few ways one could
> accomplish this, but I wanted to ask if there is an explanation in the
> manual or a tutorial that I am just missing. (Can someone point me in the
> right direction)
>
> 1. I searched the archives and saw some old posts regarding using other
> programs.
> 2. One could manually add/change things
> 3+????
>
> Not necessarily looking for a step by step but a push in the right
> direction.
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Received on Mon Sep 10 2012 - 12:00:02 PDT
