[Dock-fans] positive energy with water molecule

[Anuradha Mittal]

The prmtop file do has WAT molecule. Below are the last few lines of
receptor pdb.

ATOM   9383  CD  GLN   612       2.411  -7.714  89.480  1.00  0.00
ATOM   9384  OE1 GLN   612       2.171  -8.868  89.108  1.00  0.00
ATOM   9385  NE2 GLN   612       1.788  -6.653  88.977  1.00  0.00
ATOM   9386 1HE2 GLN   612       1.089  -6.775  88.258  1.00  0.00
ATOM   9387 2HE2 GLN   612       2.016  -5.729  89.316  1.00  0.00
ATOM   9388  C   GLN   612       3.390  -5.182  93.653  1.00  0.00
ATOM   9389  O   GLN   612       3.491  -4.025  93.202  1.00  0.00
ATOM   9390  OXT GLN   612       2.863  -5.448  94.752  1.00  0.00
TER
ATOM   9391  O   WAT   613       4.178 -24.832 113.225  1.00  0.00
ATOM   9392  H1  WAT   613       5.135 -24.832 113.225  1.00  0.00
ATOM   9393  H2  WAT   613       3.938 -23.905 113.225  1.00  0.00
TER
ATOM   9394  O   WAT   614      51.097 -24.833  93.154  1.00  0.00
ATOM   9395  H1  WAT   614      52.054 -24.833  93.154  1.00  0.00
ATOM   9396  H2  WAT   614      50.857 -23.906  93.154  1.00  0.00
TER
END

The log file from dock6 gives this error:

bad number of bonds to C: 9390 1; using default carbon parameters
bad number of bonds to O*: 9434 0; using default oxygen parameters
bad number of bonds to O*: 9437 0; using default oxygen parameters

But there is no atom number 9434 and 9437 in pdb. Also, 9390 is not C, but O
of terminal Gln.

There are no other errors in dock6 log file.

Thanks
Anu


On Tue, Sep 9, 2008 at 1:10 AM, Scott Brozell <sbrozell at scripps.edu> wrote:

> Hi,
>
> On Mon, 8 Sep 2008, Anuradha Mittal wrote:
>
> > I am carrying out amberdock recoring calculations on a set of ligands.
> There
> > is a water molecule in the protein that I need to include while
> performing
> > the calculations.
> >
> > I am getting positive amber score for all the ligands. However if I
> remove
> > that water molecule all scores are negative. I prepared all structures
> using
> > sybyl but did change the nomenclature according to amber.
>
> What exactly does this mean ?
> Did you execute prepare_amber.pl ?
> If a water exists in the receptor pdb file argument to prepare_amber.pl
> then a TIP3P water model will be used.  So if the pdb has, e.g.,
> TER
> ATOM  30277  O   WAT  9659       0.444  -0.413 -43.191  1.00  0.00
> ATOM  30278  H1  WAT  9659      -0.232  -0.514 -42.521  1.00  0.00
> ATOM  30279  H2  WAT  9659       1.267  -0.569 -42.727  1.00  0.00
> then the prmtop will have a WAT residue.
>
> > What am I doing wrong here? Is it that Amber-dock doesn't support water
> > molecules? Or do I need to explicitly define the parameters for water?
> Any
> > suggestions?
>
> Since there is a change in the Amber rescores with and without water,
> the water seems to be there.  The simple diagnostic route starts with
> visualization, and probably the extra details from verbose dock6 (-v)
> calculations will be informative.  The most likely source of the positive
> energy is a clash which should show up in both of the above, but the phase
> space of possibilities is large.
>
> Scott
>
>
>
> Scott
>
>
>
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