Hell my friend, i dont need any of this messages from all the members of this board, please help alert the board, its bored reading them all, i want to unsubscribe from the group
Yang Ye <[EMAIL PROTECTED]> wrote: it could not be possible since amber force field doesn't parameterized NLYN. alternative, use ACE/NME to cap the peptide. On 11/9/2007 7:36 PM, Hu Zhongqiao wrote: > > Hi, > > > > I am using amber force field in Gromacs. The protein I simulated is > the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be > neutral. According to rules using Amber in Gromacs, neutral lysine > should be named to LYN. Everything goes smoothly except the N-terminal > lysine residue. It should carry +1 unit charge due to its location. > According to the rules, I should rename this residue as NLYN. But I > can not find NLYN in ffamber*.rtp. In other words, error will appear > if I do so. I did not get response from Dear Dr. Eric J. Sorin who > establish amber port into gromacs. So anyone knows how to set > N-terminal lysine residue carry +1, not +2 unit charges using Amber FF > in gmx? > > > > Zhongqiao > > > > National University of Singapore > > ------------------------------------------------------------------------ > > _______________________________________________ > 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 _______________________________________________ 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 __________________________________________________ Do You Yahoo!? Tired of spam? Yahoo! Mail has the best spam protection around http://mail.yahoo.com
_______________________________________________ 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