On Sat, Jun 29, 2013 at 11:27 AM, Maryam Hamzehee
<maryam_h_7860.yahoo.com>wrote:
> Dear Amber list
>
> I am trying to do mutation in one of the residues of my receptor (I mean
> mutation to an amino acid other than alanine) and calculate the binding
> free energy for the complex of ligand-receptor, similar to the alanine
> scanning implemented in Amber package. I found no tutorials in this case or
> in amber archives. Is it possible to mutate to any amino acid and use the
> corresponding wild type trajectory file for calculating binding energy like
> the one presented in tutorial of MM-PBSA for alanine scanning.
>
> Any help in this regard would be highly appreciated.
>
MMPBSA.py also supports in-place mutation to Glycine as of AmberTools 13.
For any other types of mutations, you will need to find another way to
perform the mutation. For example, you can write a PDB of your system,
change the residue name of the residue you want mutated (and delete the
side-chain atoms), run the PDB back through tleap to get a new topology,
then run dynamics on the new system.
If you want to do the mutation in-place and re-use the dynamics of the
original system, you will need to find some other software that will do
this (or you can write out a PDB for each frame in your trajectory, process
the PDB so leap will recognize it, use leap to introduce the mutation and
write out a new PDB, then use cpptraj to combine them back into a
trajectory for MMPBSA.py to process).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Sat Jun 29 2013 - 11:00:02 PDT
