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 <[EMAIL PROTECTED]>: > 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 <[EMAIL PROTECTED]> 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 <[EMAIL PROTECTED]> > > 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 <[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 > > > > > > > > > > > -- > > 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 > > > > > > -- > 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 [EMAIL PROTECTED] | (540) 231-9080 http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/ ======================================== _______________________________________________ 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
