Re: [AMBER] methyl group at the N-terminal

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Fri, 19 Jun 2009 13:12:36 +0100

Dear Francesca,

> I would like to know whether it is possible or not to substitute one
> of the hydrogen at the N-terminal of a protein with a CH3 group
> using leap, and eventually how.

You will have to develop a new fragment for your (+)MeNH2-terminal aminoacid.

You could try to follow what is done .
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#16
  and
http://q4md-forcefieldtools.org/Tutorial/Tutorial-3.php#24
replacing (+)NH3-Me (methylammonium) by (+)MeNH2-Me to see if this works.

regards, Francois



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Received on Mon Jul 06 2009 - 10:07:31 PDT