Thanks very much.
Sorry for the mistake, Actually, I'm trying to use mm_pbsa.pl.
In the .DECOMP section of the input, I have to set the receptor and
ligand residues.
I don't know how I can set, as receptor, the residues from 1 to 310 and
from 482 to 483 (2 ions of Mg2+).
Can You help me?
Chiara
On Thu, 2012-09-13 at 10:56 -0400, Jason Swails wrote:
> 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
>
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Received on Thu Sep 13 2012 - 08:30:03 PDT
