Hi!<br>It is actually a phosphorylated serine!! So I am wondering if GMX has any special building block for handling such special cases?<br>Jayant<br><br><br><br><div class="gmail_quote">On Wed, Apr 9, 2008 at 12:26 AM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">Darn, forget that post, I wasn't reading clearly. Too early here. It's<br>
part of a phosphorylated residue, you could've at least mentioned the<br>
residue to go with it. There's some stuff on the contributions pages<br>
of the gromacs site about phosphorylated residues. Have a look there.<br>
<br>
Sorry for the previous babbling... The reference to the wiki still goes though<br>
<br>
Cheers,<br>
<font color="#888888"><br>
Tsjerk<br>
</font><div><div></div><div class="Wj3C7c"><br>
<br>
<br>
On Wed, Apr 9, 2008 at 9:24 AM, Tsjerk Wassenaar <<a href="mailto:tsjerkw@gmail.com">tsjerkw@gmail.com</a>> wrote:<br>
> Hi Jayant,<br>
><br>
> PO3 seems to me the anion of metaphosphoric acid, not much to do with<br>
> phosphoric acid. The latter could be sort of extracted from phosphoric<br>
> acid containing residues, although that doesn't give guarantees for<br>
> good behaviour. Also, I wouldn't count on the PO4 parameters thus<br>
> extracted to have much to do with PO3. Very likely that the atomic<br>
> charges are quite different, but maybe LJ parameters too.<br>
><br>
> Have a look at<br>
><br>
> <a href="http://wiki.gromacs.org/index.php/Parameterization" target="_blank">http://wiki.gromacs.org/index.php/Parameterization</a><br>
><br>
> Cheers,<br>
><br>
> Tsjerk<br>
><br>
><br>
><br>
> On Wed, Apr 9, 2008 at 3:44 AM, jayant james <<a href="mailto:jayant.james@gmail.com">jayant.james@gmail.com</a>> wrote:<br>
> > Hi !<br>
> > I am attempting to simulate a protein that is phosphorylated below is a part<br>
> > of the PDF file<br>
> > HETATM 460 P PO3 A 200 14.995 1.523 4.011 1.00 0.89<br>
> > P<br>
> > HETATM 461 O1 PO3 A 200 14.287 1.882 5.272 1.00 1.16<br>
> > O<br>
> > HETATM 462 O2 PO3 A 200 15.841 0.179 4.048 1.00 0.77<br>
> > O<br>
> > HETATM 463 O3 PO3 A 200 14.134 1.500 2.694 1.00 0.97<br>
> > O<br>
> > HETATM 464 P PO3 A 201 13.207 -1.138 -1.342 1.00 1.31<br>
> > P<br>
> > HETATM 465 O1 PO3 A 201 12.997 -2.551 -0.914 1.00 1.43<br>
> > O<br>
> > HETATM 466 O2 PO3 A 201 11.918 -0.211 -1.324 1.00 1.47<br>
> > O<br>
> > HETATM 467 O3 PO3 A 201 13.927 -0.914 -2.727 1.00 1.41<br>
> > O<br>
> ><br>
> > but upon executing pdb2gmx of the PDB file I get an error<br>
> > -----------------------------------------------------------------<br>
> > Fatal error:<br>
> > Residue 'PO3' not found in residue topology database<br>
> > ------------------------------------------------------------------<br>
> ><br>
> > I do know that DNA can be simulated in GROMOS (option 0 of pdb2gmx). So I am<br>
> > wondering how to overcome the above error.<br>
> ><br>
> > Awaiting suggestions<br>
> > Thanks<br>
> > Jayant<br>
> ><br>
> ><br>
> > --<br>
> > Jayasundar Jayant James<br>
> ><br>
> > <a href="http://www.chick.com/reading/tracts/0096/0096_01.asp" target="_blank">www.chick.com/reading/tracts/0096/0096_01.asp</a>)<br>
> > Residence -24935864, cell-9841042164<br>
> > _______________________________________________<br>
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> ><br>
><br>
><br>
><br>
> --<br>
> Tsjerk A. Wassenaar, Ph.D.<br>
> Junior UD (post-doc)<br>
> Biomolecular NMR, Bijvoet Center<br>
> Utrecht University<br>
> Padualaan 8<br>
> 3584 CH Utrecht<br>
> The Netherlands<br>
> P: +31-30-2539931<br>
> F: +31-30-2537623<br>
><br>
<br>
<br>
<br>
--<br>
Tsjerk A. Wassenaar, Ph.D.<br>
Junior UD (post-doc)<br>
Biomolecular NMR, Bijvoet Center<br>
Utrecht University<br>
Padualaan 8<br>
3584 CH Utrecht<br>
The Netherlands<br>
P: +31-30-2539931<br>
F: +31-30-2537623<br>
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</div></div></blockquote></div><br><br clear="all"><br>-- <br>Jayasundar Jayant James<br><br><a href="http://www.chick.com/reading/tracts/0096/0096_01.asp">www.chick.com/reading/tracts/0096/0096_01.asp</a>) <br>Residence -24935864, cell-9841042164