On Mon, Oct 31, 2011 at 2:21 AM, James Starlight <jmsstarli...@gmail.com> wrote: > Dear PyMol users! > > I want to prepare my pdb structure for MD simulation with gromacs
You may ask in gmx list. > > 1- I want to place some CAP groups like ACE or NH2 to N and C termii of 1 > and last residue of my protein, respectyally. > > I found possible option for this in the build- amono acids > buit creted via this way ACE or NH2 groups were placed in the same label w\o > links to specified atoms ( e.g I've selected C atom from 1 residue and tried > to build ACE on this place) Try: pdb2gmx -ter > > So how I could merge new groups with existing atoms of the specified > residues in desired location? > > 2- I want to orient my protein along desired axis. How it could be done? Try: editconf > > Thanks, > James > > ------------------------------------------------------------------------------ > Get your Android app more play: Bring it to the BlackBerry PlayBook > in minutes. BlackBerry App World™ now supports Android™ Apps > for the BlackBerry® PlayBook™. Discover just how easy and simple > it is! http://p.sf.net/sfu/android-dev2dev > > _______________________________________________ > PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) > Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users > Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net > ------------------------------------------------------------------------------ Get your Android app more play: Bring it to the BlackBerry PlayBook in minutes. BlackBerry App World™ now supports Android™ Apps for the BlackBerry® PlayBook™. Discover just how easy and simple it is! http://p.sf.net/sfu/android-dev2dev _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
