VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Wed Jul 02 2008 - 07:52:43 CDT

It's psfgen doing this work behind the scenes; psfgen, in turn, builds
the side chain based on the internal coordinate definition of the
topology file (which specifies one unique rotamer). In the case of
mutator, any atoms with names in the new residue matching those from the
old residue are retained, and the remainder built from internal
coordinate entries. So, the answer to your question is "whatever rotamer
the topology file specifies, unless there are retained atoms from the
old residue that override this.

Note that mutator *does not* perform a minimization of the new residue,
so whatever structure came directly out of mutator *is* the structure
"before energy minimization by the vmd mutator". This is the most
definitive answer to the which rotamer question -- it's whatever rotamer
is in the output. Mutator is not a substitute for scwrl, or an
equilibration.

Best,
Peter

S. Jamal Rahi wrote:
> To whom it may concern:
>
> We have used VMD's mutator plugin to mutate an amino acid residue in our
> protein, whose energy we minimize after the mutation, and so on.
>
> For various reasons now we need to find out which rotamer was plugged in
> before energy minimization by the vmd mutator. Unfortunately, this
> information seems not be retrievable anywhere.
>
> Can somebody tell us which rotamer it is? If there is another software
> working behind the scenes, which rotamer does that software assign to
> the new amino acid side chain?
>
> Sincerely,
> S. Jamal Rahi
>
>