Re: [AMBER] MMPBSA.pl masks

From: Chiara Pallara <chiara.pallara.bsc.es>
Date: Thu, 13 Sep 2012 17:30:09 +0200

I try to create the input for MMPBSA.py but It seems it does not
recognize my mask
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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Received on Thu Sep 13 2012 - 09:00:04 PDT
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