AMBER Archive (2009)

Subject: Re: [AMBER] modifying LYN

From: Marius Retegan (marius.s.retegan_at_gmail.com)
Date: Tue Mar 31 2009 - 11:58:06 CDT

Thank you
I forgot about CYX.
Marius

On Tue, Mar 31, 2009 at 5:41 PM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

> Dear Marius,
>
> I have a cyclic peptide comprising of 10 amino acids, four of them being
>> lysine residues. On the neutral lysine residues, I want remove one of the
>> hydrogen atoms from the NZ atom in order to be able to connect the LYN
>> residue with another amino acid. My question is how can I modify the LYN
>> residue in order to make it accept 3 connections.
>>
>
> This means you want LYN to have three connections as CYX as three
> connections.
>
> - Load leaprc.ff99 or leaprc.ff99SB in LEap
>
> - Check for the CYX residue involved in a disulfide bridge:
> desc CYX
> desc CYX.1
>
> - Apply the same rule for LYN; i.e. define three atoms as connect0,
> connect1 & connect2.
>
> This means you will have to create a new LYN residue i.e. a new LYN
> fragment. You can use R.E.D. for that.
>
> regards, Francois
>
>
>
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