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 [email protected] > 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 [email protected] 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
