ACE for the N-termail and NME for the C-terminal. They are neutral. You
can do so with aids from PyMol...
Regards,
Yang Ye
On 11/9/2007 9:50 PM, Hu Zhongqiao wrote:
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 <[EMAIL PROTECTED]>
Subject: Re: [gmx-users] How to set N-terminal lysine carry only +1
unit charge?
To: Discussion list for GROMACS users <[email protected]>
Message-ID: <[EMAIL PROTECTED]>
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
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