On Thu, Sep 13, 2012 at 11:00 AM, Chiara Pallara <chiara.pallara.bsc.es>wrote:
> 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
>
If you try using MMPBSA.py, this mask will be determined automatically (the
only requirement to automatic mask determination is that the ligand
residues appear continuously inside the complex -- receptor residues do not
have to be continuous). This should simplify the input file.
Since I don't have much experience with the perl version, my suggestion is
to look at some of the example files and try to adapt them to your system
until someone more knowledgeable is able to respond if you don't want to
use MMPBSA.py.
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 - 08:30:04 PDT
