AMBER Archive (2009)

Subject: Re: [AMBER] modifying LYN

From: FyD (fyd_at_q4md-forcefieldtools.org)
Date: Tue Mar 31 2009 - 10:41:56 CDT

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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