Hello,
On Thu, Sep 13, 2012 at 8:24 AM, Chiara Pallara <chiara.pallara.bsc.es>wrote:
> Hi Amber,
> I'm trying to perform a binding energy decomposition (on a pairwise
> per-residue basis) on a protein-protein complex with Amber MMPBSA.pl
> script. I don't know how I can set my receptor/ligand residues masks
> since they correspond to no-consecutive residues.
> Thanks a lot for your help!
>
This is a little confusing. There are two MM/PBSA scripts in Amber (one in
AmberTools, one in Amber). One is MMPBSA.py, and the other is mm_pbsa.pl.
Only MMPBSA.py uses Amber masks (and requires continuous residues for
proper mask guessing). Therefore, I'm going to assume you're using
MMPBSA.py.
Let's pretend your complex is 100 residues. Let's also pretend that you
have 2 ligand sequences (this can happen if you have a dimer, for
instance). This would mean that the first 50 residues are in the first
monomer and the second 50 residues are in the second monomer. If the
ligand is the last 5 residues in each monomer, then your receptor residues
would be residues 1-45 and 51 to 95. Your ligand residues would be 46 to
50 and 96 to 100. Your receptor_mask and ligand_mask would then be
receptor_mask = :1-45,51-95
ligand_mask = :46-50,96-100
If you are you are using the mm_pbsa.pl script, the input is different.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 13 2012 - 08:00:03 PDT
