AMBER Archive (2009)

Subject: [AMBER] LYN again

From: Marius Retegan (marius.s.retegan_at_gmail.com)
Date: Sat Apr 04 2009 - 08:12:09 CDT

Hello,

A few days ago I asked on the amber list about how to modify a neutral
lysine in order to make another bond.
The system that I study is something like this:
                                   O O
                                    || ||
protein - Lys - N(NZ) - C - linker - C - N(NZ) - Lys - protein
                       | |

                      H H

Basically the NZ atom of the lysine residue has one hydrogen attached to it
and enters in a peptidic bond with the CO group of the linker.

I've managed to get all the bonds in xleap, but now comes the big problem.
First I was interested in determining the charge for the lysine residues,
but since I've removed an hydrogen they are now -1. Unfortunately I don't
have access to the JCC paper where the procedure of getting charges for
amino acids is described (for example CYX).

It would help me alot if someone could suggest a way on how to derive the
charges for a charged amino acid and secoundly, should I constrain the
charges on the CO moieties of the linker (I've seen that for almost all
amino acids the atoms that enter a peptidic group have constrained charges).

Thank you
Marius
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