Indeed, there are .hdb entries for nucleic acids in the Amber ports. I wasn't sure, but grepped for the wrong thing, so yes, they're there!
Sorry for the mistake. -Justin Quoting Mark Abraham <[EMAIL PROTECTED]>: > Vigneshwar Ramakrishnan wrote: > > 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. > > No you're both (potentially) right. > > > On Fri, May 2, 2008 at 12:09 AM, Justin A. Lemkul <[EMAIL PROTECTED] > > <mailto:[EMAIL PROTECTED]>> wrote: > > 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. > > If the port of the AMBER force fields to GROMACS have suitable .hdb > files, then pdb2gmx can deal with the problem. > > Mark > _______________________________________________ > 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
