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

[Hu Zhongqiao]

Thanks, Yang Ye.

You mean that I put an additional ACE or NME on the N-terminal lysine
residue?

zhongqiao


> Message: 3
> Date: Fri, 09 Nov 2007 20:03:21 +0800
> From: Yang Ye <leafyoung at yahoo.com>
> Subject: Re: [gmx-users] How to set N-terminal lysine carry only +1
> 	unit	charge?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <47344C89.6040803 at yahoo.com>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> 
> 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