Re: [AMBER] Building a new structure!

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Thu, 24 Jan 2013 08:51:33 +0100

Dear Ibrahim,

> I am trying to simulate the Schiff base for my protein in which
> lysine is binding the fructose molecule through a covalent bond NZ-C1 of
> fructose. Can I use xleap to build this structure and how. What I have in
> my hand that I should separate lysine residue from the protein and attach
> it to fructose and then re-ligate, is it correct. I do not know how can
> xleap can do.

If I understand you you are interested in constructing a new residue
i.e. a L-lysine connected to D-fructose through an imine bond.

You can use R.E.D. and/or R.E.D. Server for this work; and you can
directly build a new central fragment for this new Lysine residue.
See for instance: http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php
                & http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
                vs http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#25

You could also consider splitting this 'lys-fructose' residue into two
building blocks. You can find examples of such an approach in R.E.DD.B.
See for instance in the sugar domain:
   http://q4md-forcefieldtools.org/REDDB/projects/F-85/
   http://q4md-forcefieldtools.org/REDDB/projects/F-72/
   http://q4md-forcefieldtools.org/REDDB/projects/F-71/

R.E.D. uses the P2N file format as input described at:
   http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#3
  & generates FF library in the mol2 file format described at:
   http://q4md-forcefieldtools.org/Tutorial/leap-mol2.php
This mol2 file format is directly usable in the LEaP prgram as described at:
http://q4md-forcefieldtools.org/Tutorial/Tutorial-1.php#1

regards, Francois



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Received on Thu Jan 24 2013 - 00:00:02 PST