[gmx-users] recognising phos group

[Justin A. Lemkul]

ffG43a1p, which was contributed to the Gromacs uploads a long time ago. 
Searching the list archives would have shown you this information.  Depending
on the version of Gromacs you're using, you may need the re-formatted files. 
The ones on the upload site are for use with an older version of Gromacs
(3.1.x, IIRC).  Contact me off-list if you'd like the re-formatted files; I
have modified them such that they can be used with the new 3.3.x series.

-Justin

Quoting jayant james <jayant.james at gmail.com>:

> 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
> > _______________________________________________
> > gmx-users mailing list    gmx-users at gromacs.org
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> > Please search the archive at http://www.gromacs.org/search before posting!
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> >
>
>
>
> --
> Jayasundar Jayant James
>
> www.chick.com/reading/tracts/0096/0096_01.asp)
> Residence -24935864, cell-9841042164
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================