ADL: WAT unrecognized

Francesco Pietra chiendarret at yahoo.com
Sun May 4 08:03:51 PDT 2008


Hi:
Thanks. The pdb from which I am used to start differs indeed from hsg1.pdb

ATOM   1513  CE2 PHE B  99      -7.379 -11.863 -10.478  1.00 37.11           C  
ATOM   1514  CZ  PHE B  99      -6.401 -11.169 -11.159  1.00 36.24           C  
HETATM 1560  O   HOH W 301      26.215   4.955 -14.294  1.00 63.94           O  
HETATM 1561  O   HOH W 303       7.924   6.974 -16.699  1.00 73.81           O 


In my pdb all ATOM, though TER between non  standard residues (safe mode for Amber9, which also does not follow the latest pdb rules for four-character atom names; don't if Amber10 was aligned with rules):

ATOM   6883  O   THR   444     -15.798  15.199  24.830
ATOM   6884  OXT THR   444     -13.937  14.328  24.944
TER   
ATOM   6885  O   WAT   445      -0.036   0.094  -2.262
ATOM   6886  H1  WAT   445       0.921   0.094  -2.262
ATOM   6887  H2  WAT   445      -0.276   1.021  -2.262
TER   
END

A question: is water deletion absolutely required by autodock4? I have strong reasons (descending from my biochemical work) for simulating docking while that crystallization water is in. Going to Amber's leap with too different names  is to search for troubles; however, ultimately my aim is at MD with the complex. I need an explicit environment with my proteins and minima can only be reached by such procedure as umbrella sampling or replica exchange..

Thanks
francesco pietra




--- On Sun, 5/4/08, Pierre-Yves Dupont <dodup64 at gmail.com> wrote:

> From: Pierre-Yves Dupont <dodup64 at gmail.com>
> Subject: Re: ADL: WAT unrecognized
> To: autodock at scripps.edu, chiendarret at yahoo.com
> Date: Sunday, May 4, 2008, 7:32 AM
> Hi,
> 
> In your selection command line, you are searching for
> residues called HOH
> and in your pdb file, your residues are called WAT. The
> write command line
> to select the water atoms in your case is :
> Residue WAT* Atom*
> 
> HOH is not a keyword in autodock, it's just the name of
> the residue in your
> file.
> 
> Cheers,
> 
> Pierre-Yves Dupont
> 
> 2008/5/4 Francesco Pietra <chiendarret at yahoo.com>:
> 
> > I am trying (1st time) to follow "Using autodock
> 4 with autodocktools: a
> > tutorial", however directly with a protein model
> of mine, already arranged
> > OK for Chimera.
> >
> > I was stuck in ADT immediately at the stage of
> selecting (Residue HOH*
> > Atom *), getting warning
> > "No new selection ::HOH*:*
> > Accepting OK, no water selected (0 Molecules(s) in a
> red background in the
> > center of the message-bar at bottom).
> >
> > Actually, the pdb loaded contains one molecule of
> water of crystallization
> > (that I had deliberately left in for docking already
> carried out with other
> > programs). The residue is called WAT, three line for O
> and the two H). Does
> > autodock4 use a different name for water residue? I
> searched along manuals
> > and archives; unable to find how non-standard residues
> are called in
> > autodock4).
> >
> > Thanks
> > francesco pietra
> >
> >
> >
> > 
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