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 <[EMAIL PROTECTED]> 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 > _______________________________________________ > gmx-users mailing list gmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
