[gmx-users] recognising phos group

[Tsjerk Wassenaar]

Darn, forget that post, I wasn't reading clearly. Too early here. It's
part of a phosphorylated residue, you could've at least mentioned the
residue to go with it. There's some stuff on the contributions pages
of the gromacs site about phosphorylated residues. Have a look there.

Sorry for the previous babbling... The reference to the wiki still goes though

Cheers,

Tsjerk



On Wed, Apr 9, 2008 at 9:24 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:
> 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
>



-- 
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