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

[Yang Ye]

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 <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
>>>       
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