[gmx-users] recognising phos group

[jayant james]

Hi!
It is actually a phosphorylated serine!! So I am wondering if GMX has any
special building block for handling such special cases?
Jayant



On Wed, Apr 9, 2008 at 12:26 AM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> 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
> _______________________________________________
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-- 
Jayasundar Jayant James

www.chick.com/reading/tracts/0096/0096_01.asp)
Residence -24935864, cell-9841042164
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