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

Yang Ye leafyoung at yahoo.com
Fri Nov 9 13:03:21 CET 2007

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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