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

[Hu Zhongqiao]

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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