On Thu, Sep 13, 2012 at 11:30 AM, Chiara Pallara <chiara.pallara.bsc.es>wrote:
> I try to create the input for MMPBSA.py but It seems it does not
> recognize my mask
>
You do not need ligand_mask or receptor_mask. The ligand residues are
continuous, and MMPBSA.py will be able to figure it out for itself.
HTH,
Jason
> This is my input:
> Pairwise GB and PB decomposition
> &general
> ligand_mask= :311-482,
> receptor_mask= :1-310,483-484,
> startframe=3000, endframe=5000, interval=10, verbose=1,
> /
> &gb
> igb=5, saltcon=0.100,
> /
> &pb
> istrng=0.100,
> /
> &decomp
> idecomp=1,
> dec_verbose=0,
> /
> This is the error:
> Warning: Input error! "483-484" is not recognized. Initialize variables
> with "="
> Thanks
> Chiara
>
> On Thu, 2012-09-13 at 11:17 -0400, Jason Swails wrote:
> > 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
> >
>
>
>
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--
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 - 09:00:06 PDT
