Hi All, I am a newbie to GROMACS, so pardon me if I am wrong.
I think pdb2gmx can handle this with amber forcefields. We just need to use the right nomenclature. I think the .hdb files for amber ff in GROMACS are already equipped with the necessary info. I am not sure why one must use an external software for adding the hydrogen atoms. If I am wrong, pls correct me. Thank you, Vignesh On Fri, May 2, 2008 at 12:09 AM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > > In terms of external software, check out OpenBabel: > http://openbabel.org/wiki/Main_Page > > There's also the H++ server, which employs Babel as part of its algorithm: > http://biophysics.cs.vt.edu/H++/index.php > > I believe H++ can handle nucleic acids. You could also do all of this > with > Gromacs, if you can come up with relevant entries in the .hdb file for > your > particular force field. Then pdb2gmx could produce the right structure > with > added hydrogens. > > -Justin > > Quoting Arijit Maitra <[EMAIL PROTECTED]>: > > > Hi All > > > > I have been trying to simulate a DNA tetramer > > d(GGGGTTTTGGGG)_2 using gromacs with amber ports. I > > have downloaded the X-ray structure from > > www.rcsb.org/pdb which has several missing hydrogen > > atoms. Can anybody advise how to plug in the missing > > atoms, e.g. with softwares or otherwise to proceed > > with the pdb2gmx command? > > > > Thanks > > Ari > > > > > > > > > > ____________________________________________________________________________________ > > Be a better friend, newshound, and > > know-it-all with Yahoo! Mobile. Try it now. > > http://mobile.yahoo.com/;_ylt=Ahu06i62sR8HDtDypao8Wcj9tAcJ > > _______________________________________________ > > 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 > > > > > > ======================================== > > 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 > -- R.Vigneshwar Graduate Student, Dept. of Chemical & Biomolecular Engg, National University of Singapore, Singapore "Strive for Excellence, Never be satisfied with the second Best!!" "The rewards of sincere resolves are highs money can never buy!"
_______________________________________________ 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