[gmx-users] recognising phos group

[Tsjerk Wassenaar]

Hi Jayant,

PO3 seems to me the anion of metaphosphoric acid, not much to do with
phosphoric acid. The latter could be sort of extracted from phosphoric
acid containing residues, although that doesn't give guarantees for
good behaviour. Also, I wouldn't count on the PO4 parameters thus
extracted to have much to do with PO3. Very likely that the atomic
charges are quite different, but maybe LJ parameters too.

Have a look at

http://wiki.gromacs.org/index.php/Parameterization

Cheers,

Tsjerk

On Wed, Apr 9, 2008 at 3:44 AM, jayant james <jayant.james at gmail.com> wrote:
> Hi !
> I am attempting to simulate a protein that is phosphorylated below is a part
> of the PDF file
> HETATM  460  P   PO3 A 200      14.995   1.523   4.011  1.00  0.89
> P
> HETATM  461  O1  PO3 A 200      14.287   1.882   5.272  1.00  1.16
> O
>  HETATM  462  O2  PO3 A 200      15.841   0.179   4.048  1.00  0.77
> O
> HETATM  463  O3  PO3 A 200      14.134   1.500   2.694  1.00  0.97
> O
> HETATM  464  P   PO3 A 201      13.207  -1.138  -1.342  1.00  1.31
> P
>  HETATM  465  O1  PO3 A 201      12.997  -2.551  -0.914  1.00  1.43
> O
> HETATM  466  O2  PO3 A 201      11.918  -0.211  -1.324  1.00  1.47
> O
> HETATM  467  O3  PO3 A 201      13.927  -0.914  -2.727  1.00  1.41
> O
>
> but upon executing pdb2gmx of the PDB file I get an error
> -----------------------------------------------------------------
> Fatal error:
> Residue 'PO3' not found in residue topology database
> ------------------------------------------------------------------
>
> I do know that DNA can be simulated in GROMOS (option 0 of pdb2gmx). So I am
> wondering how to overcome the above error.
>
> Awaiting suggestions
> Thanks
> Jayant
>
>
> --
> Jayasundar Jayant James
>
> www.chick.com/reading/tracts/0096/0096_01.asp)
> Residence -24935864, cell-9841042164
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-- 
Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623