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 <[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
>
>
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