On Fri, Apr 22, 2016 at 12:52 PM, Jag Silwal <jagsilwal.gmail.com> wrote:
> Dear all,
>
> I calculate the decomposition energy of some residues in a protein complex.
> Now I want to mutate these residues one at a time as well as mutate
> multiple resides at the same time so that I could study the change in
> decomposition energy due to mutation.
>
> What would be the best way to approach such calculations? Can I simply take
> the wild type complex..................mutate as desired
> ..................create new topology files using tleap and then use those
> to calculate new decomposition energy? I was not sure on this because based
> on the command the coordinate file (.mdcrd) is from the wild type.
>
> May be I am just over thinking but any insights would be very helpful.
>
>
> $AMBERHOME/bin/MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -do
> FINAL_DECOMP_MMPBSA.dat -sp ras-raf_solvated.prmtop -cp ras-raf.prmtop -rp
> ras.prmtop -lp raf.prmtop -y *.mdcrd
>
The only automatic mutations that MMPBSA.py will do is mutating residues
to alanine or glycine. Any other mutation analyses you want to do will
require running a separate trajectory on that mutant (and note that reusing
the same trajectory assumes that the mutation does not affect dynamics).
In both cases you need new topology files for the mutant systems.
Furthermore, MMPBSA.py can only mutate one residue at a time. So if you
want to mutate multiple residues to alanine or glycine, you have to do them
one at a time.
But if your intention is to rerun the dynamics, anyway, then there are no
special "tricks" to doing what you want to do. Just prepare and run each
mutant separately.
HTH,
Jason
--
Jason M. Swails
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Received on Sat Apr 23 2016 - 22:00:03 PDT
