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<BR><BR><B><I>Yang Ye <leafyoung@yahoo.com></I></B> wrote: <BLOCKQUOTE class=replbq style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #1010ff 2px solid">it could not be possible since amber force field doesn't parameterized <BR>NLYN. alternative, use ACE/NME to cap the peptide.<BR><BR>On 11/9/2007 7:36 PM, Hu Zhongqiao wrote:<BR>><BR>> Hi,<BR>><BR>> <BR>><BR>> I am using amber force field in Gromacs. The protein I simulated is <BR>> the lysozyme (PDBID: 1HEL). I want to set all lysine residues to be <BR>> neutral. According to rules using Amber in Gromacs, neutral lysine <BR>> should be named to LYN. Everything goes smoothly except the N-terminal <BR>> lysine residue. It should carry +1 unit charge due to its location. <BR>> According to the rules, I
should rename this residue as NLYN. But I <BR>> can not find NLYN in ffamber*.rtp. In other words, error will appear <BR>> if I do so. I did not get response from Dear Dr. Eric J. Sorin who <BR>> establish amber port into gromacs. So anyone knows how to set <BR>> N-terminal lysine residue carry +1, not +2 unit charges using Amber FF <BR>> in gmx?<BR>><BR>> <BR>><BR>> Zhongqiao<BR>><BR>> <BR>><BR>> National University of Singapore<BR>><BR>> ------------------------------------------------------------------------<BR>><BR>> _______________________________________________<BR>> gmx-users mailing list gmx-users@gromacs.org<BR>> http://www.gromacs.org/mailman/listinfo/gmx-users<BR>> Please search the archive at http://www.gromacs.org/search before posting!<BR>> Please don't post (un)subscribe requests to the list. Use the <BR>> www interface or send it to gmx-users-request@gromacs.org.<BR>> Can't post? Read
http://www.gromacs.org/mailing_lists/users.php<BR><BR>_______________________________________________<BR>gmx-users mailing list gmx-users@gromacs.org<BR>http://www.gromacs.org/mailman/listinfo/gmx-users<BR>Please search the archive at http://www.gromacs.org/search before posting!<BR>Please don't post (un)subscribe requests to the list. Use the <BR>www interface or send it to gmx-users-request@gromacs.org.<BR>Can't post? Read http://www.gromacs.org/mailing_lists/users.php<BR></BLOCKQUOTE><BR><p> __________________________________________________<br>Do You Yahoo!?<br>Tired of spam? Yahoo! Mail has the best spam protection around <br>http://mail.yahoo.com