[gmx-users] How to set N-terminal lysine carry only +1 unit charge?

[Yang Ye]

DIY on the admin panel

http://www.gromacs.org/index.php?option=com_wrapper&Itemid=83

On 11/9/2007 11:04 PM, Henry O Ify wrote:
> 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 <leafyoung at yahoo.com>/* 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 at 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 gmx-users-request at gromacs.org.
>     > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
>     _______________________________________________
>     gmx-users mailing list gmx-users at 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 gmx-users-request at gromacs.org.
>     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 at 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 gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php